Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbs Working: n-9-21.cluster.ucsf.bkslab.org:/scratch/xiaobo/132203/xbs-8058115.45 Result: /scratch/xiaobo/132203/xbs-8058115.45 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/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/xbc/inputs/xbs mkdir: created directory `/scratch/xiaobo/132203' mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45' /scratch/xiaobo/132203/xbs-8058115.45 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/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/132203/xbs-8058115.45/working' mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/protonate' Storing results in /scratch/xiaobo/132203/xbs-8058115.45/finished Working in /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 /scratch/xiaobo/132203/xbs-8058115.45/working/protonate /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Using inputs as protomers/tautomers. No processing done 489 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/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Bulk generating 3D conformations all protomers in /scratch/xiaobo/132203/xbs-8058115.45/working/3D mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/132203/xbs-8058115.45/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 ZINC000900019144 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building' mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000900019144 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/1 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2)c(C(C)=O)s1) `ZINC000900019144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900019144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900019144 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2)c(C(C)=O)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 6, 14, 14, 18, 18, 18] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900019144 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/finished' Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900019144 Building ZINC000900031097 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900031097 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/2 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1) `ZINC000900031097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900031097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031097 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20] 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]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/3 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1) `ZINC000900031097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900031097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031097 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900031097 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 Building ZINC000900031097 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900031097 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 2) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1) `ZINC000900031097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900031097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031097 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20] 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]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 3) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1) `ZINC000900031097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900031097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031097 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900031097 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031097 Building ZINC000900031098 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900031098 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/4 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1) `ZINC000900031098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900031098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031098 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/5 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1) `ZINC000900031098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900031098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031098 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900031098 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 Building ZINC000900031098 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900031098 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 4) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1) `ZINC000900031098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900031098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031098 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 5) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1) `ZINC000900031098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900031098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900031098 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 19, 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]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900031098 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900031098 Building ZINC000900059425 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900059425 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/6 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1) `ZINC000900059425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900059425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900059425 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 15, 15, 15, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 15, 19, 19, 19, 7] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/7 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1) `ZINC000900059425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900059425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900059425 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 15, 15, 15, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 15, 19, 19, 19, 7] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900059425 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 Building ZINC000900059425 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900059425 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 6) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1) `ZINC000900059425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900059425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900059425 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 15, 15, 15, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 15, 19, 19, 19, 7] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 7) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1) `ZINC000900059425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900059425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900059425 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2cccs2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 15, 15, 15, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 15, 19, 19, 19, 7] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900059425 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900059425 Building ZINC000900050164 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050164 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/8 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000900050164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900050164 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 15] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/9 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000900050164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900050164 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 15] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050164 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 Building ZINC000900050164 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050164 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 8) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000900050164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900050164 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 15] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 9) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000900050164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900050164 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 15] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050164 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050164 Building ZINC000900050480 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050480 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/10 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050480 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 9, 9, 9, 9, 21] 40 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]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/11 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050480 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 13, 13, 13, 13, 20] 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]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050480 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 Building ZINC000900050480 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050480 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 10) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050480 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 9, 9, 9, 9, 21] 40 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]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 11) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050480 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 13, 13, 13, 13, 20] 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]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050480 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050480 Building ZINC000900050482 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050482 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/12 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050482 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 13, 13, 13, 13, 20] 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]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/13 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050482 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 9, 9, 9, 9, 21] 40 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]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050482 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 Building ZINC000900050482 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050482 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 12) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050482 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 8, 13, 13, 13, 13, 20] 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]) total number of confs: 90 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 13) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F) `ZINC000900050482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900050482 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc2ccccc2n1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 9, 9, 9, 9, 21] 40 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]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050482 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050482 Building ZINC000900050620 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050620 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/14 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000900050620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900050620 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/15 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000900050620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900050620 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 10, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050620 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 Building ZINC000900050620 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900050620 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 14) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000900050620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900050620 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 15) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000900050620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900050620 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 10, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900050620 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900050620 Building ZINC000900066551 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900066551 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/16 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1) `ZINC000900066551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900066551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900066551 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 11, 18, 18, 12, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 18, 18, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/17 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1) `ZINC000900066551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900066551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900066551 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 11, 18, 18, 12, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 18, 18, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900066551 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 Building ZINC000900066551 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900066551 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 16) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1) `ZINC000900066551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900066551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900066551 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 11, 18, 18, 12, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 18, 18, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 17) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1) `ZINC000900066551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900066551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900066551 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc1n2CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 11, 18, 18, 12, 11, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 18, 18, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900066551 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900066551 Building ZINC000900063939 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900063939 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/18 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F) `ZINC000900063939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900063939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900063939 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 16, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/19 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F) `ZINC000900063939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900063939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900063939 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 4, 6, 6, 6, 14, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 2, 6, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900063939 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 Building ZINC000900063939 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900063939 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 18) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F) `ZINC000900063939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900063939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900063939 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 16, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 19) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F) `ZINC000900063939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900063939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900063939 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 4, 6, 6, 6, 14, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 2, 6, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900063939 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900063939 Building ZINC000900081341 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900081341 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/20 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F) `ZINC000900081341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900081341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900081341 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 9, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/21 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F) `ZINC000900081341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900081341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900081341 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900081341 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 Building ZINC000900081341 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900081341 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 20) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F) `ZINC000900081341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900081341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900081341 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 9, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 21) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F) `ZINC000900081341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900081341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900081341 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900081341 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900081341 Building ZINC000900085968 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900085968 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/22 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1) `ZINC000900085968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900085968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900085968 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 15, 18, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/23 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1) `ZINC000900085968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900085968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900085968 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 14, 18, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900085968 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 Building ZINC000900085968 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900085968 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 22) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1) `ZINC000900085968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900085968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900085968 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 15, 18, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 23) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1) `ZINC000900085968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900085968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900085968 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nccn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 14, 18, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900085968 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900085968 Building ZINC000900114169 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900114169 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/24 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1) `ZINC000900114169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900114169 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/25 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1) `ZINC000900114169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900114169 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900114169 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 Building ZINC000900114169 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900114169 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 24) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1) `ZINC000900114169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900114169 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 25) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1) `ZINC000900114169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900114169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900114169 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900114169 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900114169 Building ZINC000900128356 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900128356 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/26 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F) `ZINC000900128356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900128356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900128356 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 11, 17, 17, 17, 14, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/27 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F) `ZINC000900128356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900128356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900128356 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 11, 17, 17, 17, 14, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900128356 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 Building ZINC000900128356 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900128356 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 26) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F) `ZINC000900128356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900128356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900128356 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 11, 17, 17, 17, 14, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 27) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F) `ZINC000900128356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900128356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900128356 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cc(Br)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 11, 17, 17, 17, 14, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900128356 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900128356 Building ZINC000900154912 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900154912 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/28 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1) `ZINC000900154912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900154912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154912 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/29 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1) `ZINC000900154912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900154912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154912 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900154912 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 Building ZINC000900154912 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900154912 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 28) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1) `ZINC000900154912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900154912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154912 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 29) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1) `ZINC000900154912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900154912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154912 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900154912 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154912 Building ZINC000900154945 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900154945 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/30 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1) `ZINC000900154945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900154945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154945 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 9, 9, 7, 9, 9, 9, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 32 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/31 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1) `ZINC000900154945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900154945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154945 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 32 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900154945 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 Building ZINC000900154945 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900154945 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 30) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1) `ZINC000900154945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900154945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154945 none CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 9, 9, 7, 9, 9, 9, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 32 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 31) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1) `ZINC000900154945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900154945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900154945 none CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 32 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900154945 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900154945 Building ZINC000900167244 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900167244 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/32 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1) `ZINC000900167244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900167244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900167244 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 6, 6, 16, 17, 17, 17, 17, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 10, 10, 10, 17, 17, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/33 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1) `ZINC000900167244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900167244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900167244 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 6, 6, 16, 17, 17, 17, 17, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 10, 10, 10, 17, 17, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900167244 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 Building ZINC000900167244 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900167244 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 32) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1) `ZINC000900167244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900167244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900167244 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 6, 6, 16, 17, 17, 17, 17, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 10, 10, 10, 17, 17, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 33) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1) `ZINC000900167244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900167244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900167244 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(OCC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 10, 6, 6, 16, 17, 17, 17, 17, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 10, 10, 10, 17, 17, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900167244 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900167244 Building ZINC000900169139 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900169139 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/34 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1) `ZINC000900169139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900169139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900169139 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 5, 5, 5, 5, 5, 15, 15, 21, 21, 15, 15, 21, 21, 21, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/35 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1) `ZINC000900169139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900169139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900169139 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900169139 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 Building ZINC000900169139 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900169139 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 34) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1) `ZINC000900169139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900169139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900169139 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 5, 5, 5, 5, 5, 15, 15, 21, 21, 15, 15, 21, 21, 21, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 35) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1) `ZINC000900169139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900169139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900169139 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(C)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 11, 11, 17, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900169139 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900169139 Building ZINC000900176892 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900176892 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/36 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1) `ZINC000900176892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900176892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900176892 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 5, 10, 10, 10, 19, 19, 19, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 10, 10, 19, 20, 20, 19, 20, 20] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/37 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1) `ZINC000900176892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900176892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900176892 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 6, 10, 10, 10, 19, 19, 19, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 10, 10, 19, 20, 20, 19, 20, 20] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900176892 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 Building ZINC000900176892 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900176892 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 36) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1) `ZINC000900176892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900176892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900176892 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 5, 10, 10, 10, 19, 19, 19, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 10, 10, 19, 20, 20, 19, 20, 20] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 37) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1) `ZINC000900176892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900176892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900176892 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 6, 10, 10, 10, 19, 19, 19, 20, 20, 19, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 10, 10, 19, 20, 20, 19, 20, 20] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900176892 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900176892 Building ZINC000900182011 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900182011 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/38 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1) `ZINC000900182011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900182011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182011 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/39 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1) `ZINC000900182011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900182011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182011 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900182011 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 Building ZINC000900182011 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900182011 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 38) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1) `ZINC000900182011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900182011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182011 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 39) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1) `ZINC000900182011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900182011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182011 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900182011 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182011 Building ZINC000900182012 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900182012 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/40 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1) `ZINC000900182012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900182012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182012 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/41 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1) `ZINC000900182012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900182012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182012 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 6, 6] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900182012 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 Building ZINC000900182012 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900182012 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 40) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1) `ZINC000900182012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900182012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182012 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 41) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1) `ZINC000900182012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900182012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900182012 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccccc3o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 6, 6] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900182012 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900182012 Building ZINC000900191291 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900191291 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/42 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1) `ZINC000900191291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900191291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900191291 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 7, 7, 7, 7, 7, 10, 13, 20, 22, 22, 22, 22, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 7, 7, 7, 10, 10, 20, 20, 22, 22, 22, 7] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/43 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1) `ZINC000900191291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900191291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900191291 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 7, 7, 7, 7, 7, 10, 13, 19, 21, 21, 21, 21, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 7, 7, 7, 10, 10, 19, 19, 21, 21, 21, 7] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900191291 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 Building ZINC000900191291 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900191291 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 42) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1) `ZINC000900191291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900191291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900191291 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 7, 7, 7, 7, 7, 10, 13, 20, 22, 22, 22, 22, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 7, 7, 7, 10, 10, 20, 20, 22, 22, 22, 7] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 43) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1) `ZINC000900191291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900191291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900191291 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 7, 7, 7, 7, 7, 10, 13, 19, 21, 21, 21, 21, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 7, 7, 7, 10, 10, 19, 19, 21, 21, 21, 7] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900191291 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900191291 Building ZINC000746132118 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746132118 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/44 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000746132118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746132118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000746132118 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 22, 37, 37, 37, 29, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 22, 22, 37, 37, 37] 38 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/45 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000746132118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746132118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000746132118 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 19, 32, 32, 32, 19, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 19, 19, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000746132118 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 Building ZINC000746132118 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000746132118 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 44) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000746132118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000746132118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000746132118 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 22, 37, 37, 37, 29, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 22, 22, 37, 37, 37] 38 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 45) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000746132118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000746132118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000746132118 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 19, 32, 32, 32, 19, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 19, 19, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000746132118 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000746132118 Building ZINC000900211171 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900211171 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/46 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1) `ZINC000900211171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900211171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900211171 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 18, 18, 5] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/47 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1) `ZINC000900211171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900211171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900211171 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900211171 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 Building ZINC000900211171 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900211171 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 46) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1) `ZINC000900211171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900211171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900211171 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 18, 18, 5] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 47) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1) `ZINC000900211171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900211171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900211171 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900211171 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900211171 Building ZINC000900237784 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900237784 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/48 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1) `ZINC000900237784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900237784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900237784 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/49 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1) `ZINC000900237784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900237784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900237784 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900237784 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 Building ZINC000900237784 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900237784 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 48) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1) `ZINC000900237784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900237784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900237784 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 49) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1) `ZINC000900237784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900237784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900237784 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 17, 17, 17, 17, 17, 17, 9] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900237784 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900237784 Building ZINC000900249161 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900249161 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/50 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1) `ZINC000900249161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900249161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900249161 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 2, 8, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 1, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/51 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1) `ZINC000900249161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900249161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900249161 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 2, 8, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900249161 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 Building ZINC000900249161 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900249161 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 50) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1) `ZINC000900249161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900249161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900249161 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 2, 8, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 1, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 51) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1) `ZINC000900249161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900249161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900249161 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Cn2ccnc2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 2, 8, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900249161 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900249161 Building ZINC000900254366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900254366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/52 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1) `ZINC000900254366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900254366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900254366 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/53 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1) `ZINC000900254366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900254366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900254366 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900254366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 Building ZINC000900254366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900254366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 52) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1) `ZINC000900254366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900254366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900254366 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 53) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1) `ZINC000900254366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900254366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900254366 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900254366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900254366 Building ZINC000900257289 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900257289 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/54 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900257289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900257289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000900257289 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 9, 9, 13, 13, 4, 9, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/55 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900257289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900257289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000900257289 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 9, 9, 13, 13, 4, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900257289 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 Building ZINC000900257289 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900257289 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 54) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900257289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900257289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000900257289 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 9, 9, 13, 13, 4, 9, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 55) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900257289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900257289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000900257289 none CCCN(CCC)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 9, 9, 13, 13, 4, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900257289 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900257289 Building ZINC000900259873 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900259873 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/56 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1) `ZINC000900259873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900259873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900259873 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 3, 3, 3, 7, 8, 10, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 18, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/57 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1) `ZINC000900259873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900259873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900259873 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 10, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 2, 8, 8, 10, 10, 17, 17, 17, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900259873 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 Building ZINC000900259873 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900259873 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 56) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1) `ZINC000900259873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900259873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900259873 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 3, 3, 3, 7, 8, 10, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 18, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 57) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1) `ZINC000900259873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900259873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900259873 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCc2ccco2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 10, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 2, 8, 8, 10, 10, 17, 17, 17, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900259873 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900259873 Building ZINC000900260810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900260810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/58 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1) `ZINC000900260810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900260810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900260810 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 43 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]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/59 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1) `ZINC000900260810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900260810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900260810 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 8, 8, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 38 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]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900260810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 Building ZINC000900260810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900260810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 58) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1) `ZINC000900260810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900260810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900260810 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 43 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]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 59) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1) `ZINC000900260810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900260810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900260810 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3ccc(Cl)cc3c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 8, 8, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 38 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]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900260810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900260810 Building ZINC000900265223 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900265223 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/60 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1) `ZINC000900265223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900265223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900265223 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 7, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/61 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1) `ZINC000900265223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900265223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900265223 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 7, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900265223 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 Building ZINC000900265223 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900265223 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 60) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1) `ZINC000900265223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900265223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900265223 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 7, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 61) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1) `ZINC000900265223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900265223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900265223 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2cccc(OC)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 7, 17, 17, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900265223 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900265223 Building ZINC000900272899 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900272899 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/62 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1) `ZINC000900272899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900272899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900272899 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 20, 21, 21, 21, 21, 21, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 20, 21, 21, 21, 21, 21, 5] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/63 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1) `ZINC000900272899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900272899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900272899 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 11, 18, 19, 19, 18, 19, 19, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 19, 19, 19, 19, 19, 5] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900272899 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 Building ZINC000900272899 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900272899 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 62) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1) `ZINC000900272899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900272899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900272899 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 20, 21, 21, 21, 21, 21, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 20, 21, 21, 21, 21, 21, 5] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 63) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1) `ZINC000900272899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900272899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900272899 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 11, 18, 19, 19, 18, 19, 19, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 19, 19, 19, 19, 19, 5] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900272899 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900272899 Building ZINC000900276208 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900276208 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/64 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1) `ZINC000900276208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900276208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900276208 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 12, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 19, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/65 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1) `ZINC000900276208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900276208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900276208 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 11, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 19, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900276208 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 Building ZINC000900276208 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900276208 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 64) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1) `ZINC000900276208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900276208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900276208 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 12, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 19, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 65) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1) `ZINC000900276208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900276208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000900276208 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2nncs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 11, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 19, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900276208 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900276208 Building ZINC000674749326 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000674749326 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/66 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1) `ZINC000674749326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000674749326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000674749326 none Cc1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 5, 1, 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, 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: [15, 15, 15, 15, 15, 9, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/67 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1) `ZINC000674749326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000674749326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000674749326 none Cc1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 5, 1, 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, 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: [15, 15, 15, 15, 15, 9, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000674749326 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 Building ZINC000674749326 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000674749326 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 66) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1) `ZINC000674749326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000674749326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000674749326 none Cc1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 5, 1, 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, 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: [15, 15, 15, 15, 15, 9, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 67) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1) `ZINC000674749326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000674749326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000674749326 none Cc1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)oc2c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 5, 1, 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, 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: [15, 15, 15, 15, 15, 9, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000674749326 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000674749326 Building ZINC000900280461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900280461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/68 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900280461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900280461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900280461 none CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 18, 7, 2, 7, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/69 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900280461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900280461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900280461 none CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 17, 7, 4, 7, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900280461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 Building ZINC000900280461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900280461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 68) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900280461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900280461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900280461 none CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 18, 18, 7, 2, 7, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 69) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC000900280461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900280461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900280461 none CCC(C)(C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 17, 7, 4, 7, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4] 50 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000900280461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900280461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900280461 Building ZINC000900281726 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900281726 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/70 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1) `ZINC000900281726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900281726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900281726 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/71 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1) `ZINC000900281726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900281726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900281726 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900281726 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 Building ZINC000900281726 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900281726 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 70) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1) `ZINC000900281726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900281726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900281726 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 71) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1) `ZINC000900281726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900281726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900281726 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(n2nc(C)cc2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 5] 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900281726 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900281726 Building ZINC000900287083 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900287083 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/72 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1) `ZINC000900287083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900287083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900287083 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 12, 8, 1, 1, 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, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 17, 9] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/73 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1) `ZINC000900287083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900287083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900287083 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 12, 8, 1, 1, 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, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 17, 9] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900287083 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 Building ZINC000900287083 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900287083 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 72) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1) `ZINC000900287083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900287083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900287083 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 12, 8, 1, 1, 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, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 17, 9] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 73) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1) `ZINC000900287083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900287083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900287083 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2[nH]c(c3ccco3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 12, 8, 1, 1, 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, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 17, 9] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900287083 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900287083 Building ZINC000900285254 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285254 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/74 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1) `ZINC000900285254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285254 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/75 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1) `ZINC000900285254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285254 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 3, 6, 15, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285254 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 Building ZINC000900285254 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285254 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 74) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1) `ZINC000900285254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285254 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 75) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1) `ZINC000900285254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285254 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 3, 6, 15, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285254 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285254 Building ZINC000900285255 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285255 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/76 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1) `ZINC000900285255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285255 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 15, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/77 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1) `ZINC000900285255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285255 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285255 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 Building ZINC000900285255 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285255 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 76) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1) `ZINC000900285255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285255 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 15, 15, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 77) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1) `ZINC000900285255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285255 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285255 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285255 Building ZINC000900285567 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285567 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/78 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1) `ZINC000900285567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285567 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 8, 16, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/79 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1) `ZINC000900285567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285567 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 2, 9, 16, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285567 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 Building ZINC000900285567 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900285567 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 78) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1) `ZINC000900285567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900285567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285567 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 8, 16, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 79) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1) `ZINC000900285567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900285567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900285567 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 2, 9, 16, 17, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900285567 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900285567 Building ZINC000900298462 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900298462 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/80 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1) `ZINC000900298462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900298462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900298462 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 6, 7, 7, 7, 19, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/81 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1) `ZINC000900298462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900298462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900298462 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 7, 17, 20, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900298462 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 Building ZINC000900298462 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900298462 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 80) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1) `ZINC000900298462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900298462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900298462 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 6, 7, 7, 7, 19, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 81) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1) `ZINC000900298462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900298462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900298462 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 7, 17, 20, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900298462 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900298462 Building ZINC000900303925 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303925 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/82 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C) `ZINC000900303925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303925 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/83 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C) `ZINC000900303925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303925 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 2, 12, 12, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303925 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 Building ZINC000900303925 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303925 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 82) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C) `ZINC000900303925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303925 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 83) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C) `ZINC000900303925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303925 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 2, 12, 12, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303925 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303925 Building ZINC000900303926 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303926 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/84 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C) `ZINC000900303926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303926 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 12, 12, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/85 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C) `ZINC000900303926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303926 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303926 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 Building ZINC000900303926 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303926 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 84) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C) `ZINC000900303926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303926 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 12, 12, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 85) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C) `ZINC000900303926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900303926 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303926 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303926 Building ZINC000900303960 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303960 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/86 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1) `ZINC000900303960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900303960 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/87 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1) `ZINC000900303960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900303960 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303960 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 Building ZINC000900303960 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900303960 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 86) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1) `ZINC000900303960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900303960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900303960 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 87) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1) `ZINC000900303960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900303960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900303960 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2cn3c(n2)CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900303960 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900303960 Building ZINC000900304230 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900304230 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/88 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1) `ZINC000900304230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900304230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900304230 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 4, 4, 4, 9, 9, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/89 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1) `ZINC000900304230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900304230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900304230 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 4, 4, 4, 8, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900304230 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 Building ZINC000900304230 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900304230 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 88) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1) `ZINC000900304230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900304230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900304230 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 4, 4, 4, 9, 9, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 89) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1) `ZINC000900304230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900304230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900304230 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cn3c(n2)CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 4, 4, 4, 8, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900304230 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900304230 Building ZINC000900316613 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900316613 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/90 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1) `ZINC000900316613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900316613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900316613 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 10, 15, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/91 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1) `ZINC000900316613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900316613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900316613 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 12, 17, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900316613 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 Building ZINC000900316613 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900316613 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 90) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1) `ZINC000900316613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900316613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900316613 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 10, 15, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 91) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1) `ZINC000900316613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900316613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900316613 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCC(C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 12, 17, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900316613 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900316613 Building ZINC000900317642 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900317642 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/92 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1) `ZINC000900317642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900317642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900317642 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 16, 16, 23, 23, 23, 23, 23, 23, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/93 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1) `ZINC000900317642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900317642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900317642 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 5, 5, 5, 5, 5, 16, 16, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900317642 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 Building ZINC000900317642 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900317642 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 92) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1) `ZINC000900317642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900317642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900317642 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 4, 4, 4, 4, 16, 16, 23, 23, 23, 23, 23, 23, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 23, 23, 23, 23, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 93) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1) `ZINC000900317642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900317642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900317642 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 5, 5, 5, 5, 5, 16, 16, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 17, 17, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900317642 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900317642 Building ZINC000900322352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/94 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322352 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 2, 11, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/95 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322352 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 2, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14] 41 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 Building ZINC000900322352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 94) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322352 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 2, 11, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 95) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322352 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 2, 9, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14] 41 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322352 Building ZINC000900322353 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322353 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/96 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322353 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 2, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/97 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322353 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 1, 11, 11, 1, 1, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18] 47 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322353 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 Building ZINC000900322353 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322353 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 96) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322353 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 2, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 97) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000900322353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322353 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 1, 11, 11, 1, 1, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18] 47 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322353 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322353 Building ZINC000900322354 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322354 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/98 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000900322354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322354 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 1, 11, 11, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10] 28 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/99 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000900322354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322354 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10] 31 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322354 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 Building ZINC000900322354 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322354 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 98) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000900322354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322354 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 1, 11, 11, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10] 28 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 99) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000900322354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900322354 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 2, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10] 31 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322354 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322354 Building ZINC000900322445 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322445 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/100 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1) `ZINC000900322445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900322445 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 20, 20, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/101 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1) `ZINC000900322445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900322445 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 20, 20, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322445 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 Building ZINC000900322445 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900322445 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 100) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1) `ZINC000900322445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900322445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900322445 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 20, 20, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 101) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1) `ZINC000900322445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900322445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000900322445 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1n[nH]c(C(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 5, 5, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 20, 20, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900322445 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900322445 Building ZINC000900323944 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900323944 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/102 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1) `ZINC000900323944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900323944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900323944 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 13, 13, 13, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/103 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1) `ZINC000900323944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900323944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900323944 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 13, 13, 13, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900323944 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 Building ZINC000900323944 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900323944 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 102) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1) `ZINC000900323944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900323944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900323944 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 13, 13, 13, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 103) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1) `ZINC000900323944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900323944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900323944 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 13, 13, 13, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900323944 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900323944 Building ZINC000900328510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900328510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/104 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C) `ZINC000900328510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900328510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900328510 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 6, 11, 11, 11, 11, 11, 4, 7, 9, 9, 8, 9, 8, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 7, 7, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/105 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C) `ZINC000900328510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900328510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900328510 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 10, 10, 10, 10, 10, 3, 6, 8, 8, 6, 8, 7, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 10, 10, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900328510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 Building ZINC000900328510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900328510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 104) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C) `ZINC000900328510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900328510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900328510 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 6, 11, 11, 11, 11, 11, 4, 7, 9, 9, 8, 9, 8, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 7, 7, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 105) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C) `ZINC000900328510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900328510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900328510 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 10, 10, 10, 10, 10, 3, 6, 8, 8, 6, 8, 7, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 10, 10, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900328510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900328510 Building ZINC000900320475 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900320475 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/106 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12) `ZINC000900320475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900320475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900320475 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 15, 21, 21, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 21, 6, 6, 6] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/107 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12) `ZINC000900320475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900320475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900320475 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 16, 21, 21, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 21, 6, 6, 6] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900320475 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 Building ZINC000900320475 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900320475 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 106) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12) `ZINC000900320475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900320475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900320475 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 15, 21, 21, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 21, 6, 6, 6] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 107) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12) `ZINC000900320475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900320475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900320475 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 16, 21, 21, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 21, 6, 6, 6] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900320475 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900320475 Building ZINC000900344946 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900344946 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/108 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1) `ZINC000900344946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900344946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900344946 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/109 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1) `ZINC000900344946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900344946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900344946 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 19, 19, 5, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 18, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900344946 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 Building ZINC000900344946 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900344946 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 108) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1) `ZINC000900344946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900344946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900344946 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 109) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1) `ZINC000900344946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900344946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900344946 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccccc2Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 19, 19, 5, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 19, 19, 18, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900344946 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900344946 Building ZINC000900345382 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900345382 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/110 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21) `ZINC000900345382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900345382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900345382 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 13, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/111 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21) `ZINC000900345382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900345382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900345382 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 14, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900345382 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 Building ZINC000900345382 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900345382 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 110) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21) `ZINC000900345382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900345382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900345382 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 13, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 111) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21) `ZINC000900345382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900345382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900345382 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 14, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900345382 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345382 Building ZINC000900345646 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900345646 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/112 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1) `ZINC000900345646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900345646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900345646 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 7, 7, 11, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/113 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1) `ZINC000900345646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900345646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900345646 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 9, 9, 14, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900345646 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 Building ZINC000900345646 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900345646 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 112) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1) `ZINC000900345646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900345646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900345646 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 7, 7, 11, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 113) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1) `ZINC000900345646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900345646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900345646 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 9, 9, 14, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900345646 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900345646 Building ZINC000900353769 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900353769 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/114 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1) `ZINC000900353769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900353769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353769 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 13, 18, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 17, 17, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/115 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1) `ZINC000900353769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900353769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353769 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 17, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900353769 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 Building ZINC000900353769 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900353769 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 114) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1) `ZINC000900353769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900353769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353769 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 13, 18, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 17, 17, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 115) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1) `ZINC000900353769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900353769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353769 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 17, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900353769 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353769 Building ZINC000900353770 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900353770 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/116 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1) `ZINC000900353770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900353770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353770 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 17, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/117 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1) `ZINC000900353770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900353770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353770 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 18, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 17, 17, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900353770 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 Building ZINC000900353770 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900353770 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 116) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1) `ZINC000900353770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900353770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353770 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 17, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 117) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1) `ZINC000900353770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900353770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900353770 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 12, 18, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 17, 17, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900353770 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900353770 Building ZINC000900371587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900371587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/118 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1) `ZINC000900371587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900371587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900371587 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 3, 3, 3, 8, 11, 11, 11, 18, 16, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/119 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1) `ZINC000900371587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900371587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900371587 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 9, 12, 12, 12, 17, 16, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 9, 17, 17, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900371587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 Building ZINC000900371587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900371587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 118) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1) `ZINC000900371587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900371587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900371587 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 3, 3, 3, 3, 3, 8, 11, 11, 11, 18, 16, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 119) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1) `ZINC000900371587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900371587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900371587 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)OCC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 9, 12, 12, 12, 17, 16, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 9, 17, 17, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900371587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900371587 Building ZINC000900379295 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900379295 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/120 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O) `ZINC000900379295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900379295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900379295 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 11, 23, 23, 23, 23] 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/121 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O) `ZINC000900379295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900379295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900379295 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 11, 23, 23, 23, 23] 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]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900379295 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 Building ZINC000900379295 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900379295 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 120) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O) `ZINC000900379295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900379295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900379295 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 11, 23, 23, 23, 23] 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 121) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O) `ZINC000900379295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900379295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900379295 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(F)(F)F)ccc1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 11, 23, 23, 23, 23] 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]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900379295 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900379295 Building ZINC000900383119 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900383119 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/122 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1) `ZINC000900383119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900383119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900383119 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 14, 20, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/123 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1) `ZINC000900383119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900383119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900383119 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 20, 21, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900383119 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 Building ZINC000900383119 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900383119 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 122) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1) `ZINC000900383119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900383119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900383119 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 14, 20, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 123) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1) `ZINC000900383119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900383119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900383119 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 5, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 20, 21, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900383119 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900383119 Building ZINC000900386881 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900386881 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/124 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1) `ZINC000900386881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900386881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900386881 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22] 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]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/125 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1) `ZINC000900386881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900386881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900386881 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22] 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]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900386881 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 Building ZINC000900386881 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900386881 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 124) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1) `ZINC000900386881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900386881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900386881 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22] 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]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 125) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1) `ZINC000900386881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900386881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900386881 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2oc(C(F)(F)F)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 5, 15, 15, 15, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 22, 22, 22] 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]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900386881 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900386881 Building ZINC000900387154 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900387154 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/126 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C) `ZINC000900387154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900387154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900387154 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 13, 17, 17, 13, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 13, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/127 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C) `ZINC000900387154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900387154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900387154 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 13, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900387154 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 Building ZINC000900387154 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900387154 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 126) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C) `ZINC000900387154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900387154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900387154 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 13, 17, 17, 13, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 13, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 127) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C) `ZINC000900387154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900387154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900387154 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 13, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900387154 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387154 Building ZINC000900387187 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900387187 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/128 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C) `ZINC000900387187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900387187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900387187 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 9, 9, 13, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/129 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C) `ZINC000900387187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900387187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900387187 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 9, 9, 13, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900387187 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 Building ZINC000900387187 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900387187 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 128) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C) `ZINC000900387187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900387187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900387187 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 9, 9, 13, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 129) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C) `ZINC000900387187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900387187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900387187 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC2CCCC2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 9, 9, 13, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900387187 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900387187 Building ZINC000900412213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900412213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/130 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1) `ZINC000900412213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900412213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900412213 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/131 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1) `ZINC000900412213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900412213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900412213 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900412213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 Building ZINC000900412213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900412213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 130) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1) `ZINC000900412213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900412213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900412213 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 131) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1) `ZINC000900412213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900412213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900412213 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2cc3ccccc3[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900412213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900412213 Building ZINC000900413486 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900413486 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/132 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1) `ZINC000900413486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900413486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900413486 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 3, 12, 13, 13, 13, 16, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 2, 12, 12, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/133 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1) `ZINC000900413486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900413486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900413486 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 2, 7, 12, 12, 12, 16, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 7, 7, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900413486 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 Building ZINC000900413486 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900413486 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 132) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1) `ZINC000900413486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900413486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900413486 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 3, 12, 13, 13, 13, 16, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 2, 12, 12, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 133) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1) `ZINC000900413486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900413486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900413486 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 2, 7, 12, 12, 12, 16, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 7, 7, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900413486 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900413486 Building ZINC000900418071 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900418071 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/134 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1) `ZINC000900418071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900418071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900418071 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 1, 10, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 18, 18, 18, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 8, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12] 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]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/135 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1) `ZINC000900418071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900418071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900418071 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 17, 17, 17, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 8, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12] 32 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]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900418071 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 Building ZINC000900418071 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900418071 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 134) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1) `ZINC000900418071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900418071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900418071 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 1, 10, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 18, 18, 18, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 8, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12] 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]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 135) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1) `ZINC000900418071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900418071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900418071 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(C(C)(C)C)cc2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 17, 17, 17, 12, 12, 8, 8, 8, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 8, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12] 32 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]) total number of confs: 132 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900418071 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900418071 Building ZINC000900429921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900429921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/136 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1) `ZINC000900429921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900429921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900429921 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 18, 18, 18, 18, 18, 18, 8, 8] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/137 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1) `ZINC000900429921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900429921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900429921 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 8, 8, 3, 5, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 18, 18, 18, 18, 18, 18, 8, 8] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900429921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 Building ZINC000900429921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900429921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 136) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1) `ZINC000900429921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900429921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900429921 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 18, 18, 18, 18, 18, 18, 8, 8] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 137) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1) `ZINC000900429921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900429921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900429921 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)Nc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 8, 8, 3, 5, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 18, 18, 18, 18, 18, 18, 8, 8] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900429921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900429921 Building ZINC000900435416 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900435416 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/138 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900435416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435416 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/139 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900435416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435416 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900435416 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 Building ZINC000900435416 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900435416 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 138) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900435416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435416 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 139) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900435416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435416 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900435416 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435416 Building ZINC000900435417 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900435417 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/140 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900435417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435417 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 41 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/141 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900435417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435417 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900435417 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 Building ZINC000900435417 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900435417 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 140) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900435417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435417 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 41 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 141) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1) `ZINC000900435417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900435417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000900435417 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccc(C)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900435417 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900435417 Building ZINC000900420086 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900420086 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/142 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900420086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900420086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900420086 none CCOCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 14, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 17, 17, 14, 14, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/143 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900420086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900420086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900420086 none CCOCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 14, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 17, 17, 14, 14, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900420086 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 Building ZINC000900420086 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900420086 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 142) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900420086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900420086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900420086 none CCOCCOc1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 14, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 17, 17, 14, 14, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 143) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900420086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900420086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900420086 none CCOCCOc1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 14, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 17, 17, 14, 14, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900420086 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900420086 Building ZINC000900447920 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447920 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/144 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447920 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/145 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447920 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447920 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 Building ZINC000900447920 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447920 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 144) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447920 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 145) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447920 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447920 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447920 Building ZINC000900447922 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447922 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/146 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447922 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/147 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447922 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447922 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 Building ZINC000900447922 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447922 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 146) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447922 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 147) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1) `ZINC000900447922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447922 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447922 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447922 Building ZINC000900447924 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447924 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/148 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447924 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 15, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 18, 19, 19, 19, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/149 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447924 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447924 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 Building ZINC000900447924 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447924 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 148) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447924 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 15, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 18, 19, 19, 19, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 149) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447924 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447924 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447924 Building ZINC000900447925 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447925 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/150 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447925 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/151 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447925 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447925 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 Building ZINC000900447925 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900447925 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 150) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900447925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447925 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 151) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1) `ZINC000900447925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900447925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900447925 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900447925 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900447925 Building ZINC000900475650 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900475650 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/152 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1) `ZINC000900475650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900475650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900475650 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 18, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/153 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1) `ZINC000900475650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900475650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900475650 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 17, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900475650 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 Building ZINC000900475650 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900475650 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 152) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1) `ZINC000900475650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900475650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900475650 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 18, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 153) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1) `ZINC000900475650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900475650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900475650 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(Sc2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 14, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 17, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900475650 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900475650 Building ZINC000900471428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900471428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/154 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1) `ZINC000900471428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900471428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900471428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 11, 16, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 16, 16, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/155 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1) `ZINC000900471428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900471428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900471428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 11, 16, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 16, 16, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900471428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 Building ZINC000900471428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900471428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 154) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1) `ZINC000900471428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900471428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900471428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 11, 16, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 16, 16, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 155) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1) `ZINC000900471428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900471428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900471428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1OCc1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 11, 16, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 16, 16, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900471428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900471428 Building ZINC000900481085 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900481085 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/156 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1) `ZINC000900481085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900481085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900481085 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/157 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1) `ZINC000900481085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900481085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900481085 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900481085 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 Building ZINC000900481085 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900481085 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 156) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1) `ZINC000900481085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900481085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900481085 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 157) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1) `ZINC000900481085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900481085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900481085 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900481085 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900481085 Building ZINC000900483763 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900483763 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/158 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC) `ZINC000900483763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900483763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900483763 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 9, 9, 4, 9, 9, 9, 9, 22, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 9, 22, 22, 23, 23, 23] 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/159 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC) `ZINC000900483763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900483763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900483763 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 22, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 9, 22, 22, 24, 24, 24] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900483763 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 Building ZINC000900483763 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900483763 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 158) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC) `ZINC000900483763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900483763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900483763 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 9, 9, 4, 9, 9, 9, 9, 22, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 9, 22, 22, 23, 23, 23] 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]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 159) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC) `ZINC000900483763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900483763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900483763 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(Br)c1COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 22, 24, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 9, 22, 22, 24, 24, 24] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900483763 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483763 Building ZINC000900483781 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900483781 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/160 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1) `ZINC000900483781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900483781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900483781 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 19, 19, 18, 19, 19, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 18, 19, 19, 18, 19, 19] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/161 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1) `ZINC000900483781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900483781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900483781 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 20, 20, 18, 20, 20, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 18, 20, 20, 18, 20, 20] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900483781 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 Building ZINC000900483781 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900483781 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 160) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1) `ZINC000900483781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900483781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900483781 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 19, 19, 18, 19, 19, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 18, 19, 19, 18, 19, 19] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 161) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1) `ZINC000900483781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900483781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900483781 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccccc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 20, 20, 18, 20, 20, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 18, 20, 20, 18, 20, 20] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900483781 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900483781 Building ZINC000900487366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900487366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/162 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1) `ZINC000900487366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900487366 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 5, 7, 7, 17, 17, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/163 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1) `ZINC000900487366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900487366 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 5, 7, 7, 17, 17, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900487366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 Building ZINC000900487366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900487366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 162) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1) `ZINC000900487366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900487366 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 5, 7, 7, 17, 17, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 163) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1) `ZINC000900487366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900487366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900487366 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(OCc2cscn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 5, 7, 7, 17, 17, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900487366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900487366 Building ZINC000900492441 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900492441 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/164 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C) `ZINC000900492441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900492441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900492441 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 14, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/165 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C) `ZINC000900492441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900492441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900492441 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 14, 18, 18, 14, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 18, 14, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900492441 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 Building ZINC000900492441 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900492441 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 164) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C) `ZINC000900492441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900492441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900492441 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 14, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 165) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C) `ZINC000900492441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900492441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900492441 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Sc2ncccn2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 14, 18, 18, 14, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 18, 14, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900492441 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900492441 Building ZINC000900494232 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900494232 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/166 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900494232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494232 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/167 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900494232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494232 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 22, 22, 22, 22, 22, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900494232 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 Building ZINC000900494232 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900494232 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 166) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900494232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494232 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 167) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900494232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494232 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 22, 22, 22, 22, 22, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900494232 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494232 Building ZINC000900494234 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900494234 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/168 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900494234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494234 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/169 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900494234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494234 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900494234 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 Building ZINC000900494234 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900494234 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 168) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900494234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494234 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 169) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900494234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900494234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900494234 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 17, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900494234 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900494234 Building ZINC000900507864 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900507864 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/170 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1) `ZINC000900507864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900507864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900507864 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 5, 8, 8, 8, 14, 14, 14, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 14, 22, 22, 22] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/171 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1) `ZINC000900507864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900507864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900507864 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 4, 9, 9, 9, 14, 14, 14, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 14, 22, 22, 22] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900507864 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 Building ZINC000900507864 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900507864 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 170) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1) `ZINC000900507864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900507864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900507864 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 5, 8, 8, 8, 14, 14, 14, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 14, 22, 22, 22] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 171) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1) `ZINC000900507864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900507864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900507864 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 4, 9, 9, 9, 14, 14, 14, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 14, 22, 22, 22] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900507864 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900507864 Building ZINC000900514491 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900514491 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/172 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1) `ZINC000900514491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900514491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900514491 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 6, 7, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 13, 13, 13, 13] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/173 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1) `ZINC000900514491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900514491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900514491 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 6, 8, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 15, 15, 15, 15] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900514491 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 Building ZINC000900514491 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900514491 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 172) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1) `ZINC000900514491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900514491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900514491 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 6, 7, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 13, 13, 13, 13] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 173) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1) `ZINC000900514491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900514491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900514491 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1)Cc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 9, 9, 6, 8, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 15, 15, 15, 15] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900514491 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900514491 Building ZINC000900522526 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522526 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/174 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1) `ZINC000900522526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900522526 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 21, 21, 12, 12, 12, 18, 18, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 12, 21, 21, 21, 21, 21, 18, 18, 12, 18, 18] 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]) total number of confs: 84 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/175 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1) `ZINC000900522526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900522526 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 21, 21, 12, 12, 12, 19, 19, 15, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 12, 21, 21, 21, 21, 21, 19, 19, 19, 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]) total number of confs: 96 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522526 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 Building ZINC000900522526 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522526 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 174) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1) `ZINC000900522526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900522526 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 21, 21, 12, 12, 12, 18, 18, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 12, 21, 21, 21, 21, 21, 18, 18, 12, 18, 18] 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]) total number of confs: 84 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 175) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1) `ZINC000900522526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900522526 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C2CC2)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 12, 12, 12, 21, 21, 12, 12, 12, 19, 19, 15, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 12, 21, 21, 21, 21, 21, 19, 19, 19, 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]) total number of confs: 96 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522526 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522526 Building ZINC000900522753 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522753 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/176 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21) `ZINC000900522753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522753 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/177 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21) `ZINC000900522753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522753 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522753 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 Building ZINC000900522753 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522753 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 176) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21) `ZINC000900522753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522753 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 177) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21) `ZINC000900522753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522753 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 8, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522753 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522753 Building ZINC000900522754 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522754 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/178 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21) `ZINC000900522754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522754 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/179 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21) `ZINC000900522754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522754 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522754 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 Building ZINC000900522754 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900522754 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 178) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21) `ZINC000900522754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900522754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522754 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 179) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21) `ZINC000900522754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900522754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900522754 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnn1[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900522754 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900522754 Building ZINC000900536976 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900536976 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/180 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1) `ZINC000900536976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900536976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900536976 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 23, 23, 19, 23, 23, 23, 11, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 23, 23, 23, 23] 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]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/181 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1) `ZINC000900536976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900536976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900536976 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 23, 23, 19, 23, 23, 23, 11, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 23, 23, 20, 23] 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]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900536976 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 Building ZINC000900536976 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900536976 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 180) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1) `ZINC000900536976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900536976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900536976 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 23, 23, 19, 23, 23, 23, 11, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 23, 23, 23, 23] 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]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 181) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1) `ZINC000900536976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900536976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000900536976 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cccc(Cl)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 23, 23, 19, 23, 23, 23, 11, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 6, 23, 23, 20, 23] 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]) total number of confs: 88 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900536976 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900536976 Building ZINC000900540694 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900540694 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/182 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C) `ZINC000900540694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900540694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900540694 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 8, 8, 13, 19, 19, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/183 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C) `ZINC000900540694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900540694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900540694 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 8, 8, 14, 19, 19, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900540694 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 Building ZINC000900540694 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900540694 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 182) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C) `ZINC000900540694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900540694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900540694 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 8, 8, 13, 19, 19, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 183) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C) `ZINC000900540694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900540694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900540694 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 8, 8, 14, 19, 19, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900540694 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900540694 Building ZINC000900551494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900551494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/184 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900551494 none CCOCCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 2, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/185 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900551494 none CCOCCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900551494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 Building ZINC000900551494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900551494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 184) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOCCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC) `ZINC000900551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900551494 none CCOCCOc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 2, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 185) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOCCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC) `ZINC000900551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900551494 none CCOCCOc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900551494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900551494 Building ZINC000900556765 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900556765 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/186 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1) `ZINC000900556765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900556765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900556765 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 9, 9, 9, 9, 9, 9, 3, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 5, 5, 7, 7, 7, 7] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/187 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1) `ZINC000900556765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900556765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900556765 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 9, 9, 9, 9, 9, 9, 3, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 5, 5, 7, 7, 7, 7] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900556765 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 Building ZINC000900556765 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900556765 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 186) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1) `ZINC000900556765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900556765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900556765 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 9, 9, 9, 9, 9, 9, 3, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 5, 5, 7, 7, 7, 7] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 187) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1) `ZINC000900556765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900556765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900556765 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 9, 9, 9, 9, 9, 9, 3, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 9, 9, 5, 5, 7, 7, 7, 7] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900556765 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900556765 Building ZINC000900557496 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900557496 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/188 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C) `ZINC000900557496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900557496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900557496 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 9, 12, 12, 12, 12, 12, 6, 12, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/189 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C) `ZINC000900557496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900557496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900557496 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 11, 11, 11, 11, 11, 4, 8, 11, 11, 8, 11, 10, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 8, 8, 11, 11, 8, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900557496 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 Building ZINC000900557496 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900557496 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 188) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C) `ZINC000900557496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900557496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900557496 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 9, 12, 12, 12, 12, 12, 6, 12, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 189) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C) `ZINC000900557496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900557496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900557496 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccn1)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 11, 11, 11, 11, 11, 4, 8, 11, 11, 8, 11, 10, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 8, 8, 11, 11, 8, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900557496 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900557496 Building ZINC000900561218 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900561218 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/190 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1) `ZINC000900561218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900561218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900561218 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 5, 5, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/191 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1) `ZINC000900561218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900561218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900561218 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 5, 5, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900561218 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 Building ZINC000900561218 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900561218 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 190) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1) `ZINC000900561218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900561218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900561218 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 5, 5, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 191) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1) `ZINC000900561218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900561218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900561218 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 5, 5, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900561218 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900561218 Building ZINC000900573909 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900573909 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/192 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1) `ZINC000900573909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900573909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900573909 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 6, 12, 18, 18, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 12, 12, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/193 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1) `ZINC000900573909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900573909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900573909 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 6, 11, 18, 18, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 11, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900573909 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 Building ZINC000900573909 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900573909 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 192) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1) `ZINC000900573909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900573909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900573909 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 6, 12, 18, 18, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 12, 12, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 193) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1) `ZINC000900573909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900573909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900573909 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccncc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 6, 11, 18, 18, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 11, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900573909 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900573909 Building ZINC000900575797 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900575797 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/194 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1) `ZINC000900575797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900575797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900575797 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 14, 17, 17, 14, 14, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/195 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1) `ZINC000900575797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900575797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900575797 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 14, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900575797 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 Building ZINC000900575797 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900575797 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 194) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1) `ZINC000900575797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900575797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900575797 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 14, 17, 17, 14, 14, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 195) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1) `ZINC000900575797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900575797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900575797 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 14, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900575797 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900575797 Building ZINC000900577580 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900577580 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/196 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1) `ZINC000900577580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900577580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900577580 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 10, 15, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/197 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1) `ZINC000900577580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900577580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900577580 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 11, 16, 16, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900577580 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 Building ZINC000900577580 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900577580 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 196) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1) `ZINC000900577580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900577580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900577580 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 10, 15, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 197) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1) `ZINC000900577580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900577580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900577580 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 11, 16, 16, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900577580 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900577580 Building ZINC000900588789 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900588789 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/198 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1) `ZINC000900588789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900588789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900588789 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 14, 14, 14, 25, 25, 25, 14, 14, 14, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/199 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1) `ZINC000900588789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900588789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900588789 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 12, 12, 12, 22, 22, 22, 12, 12, 12, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 19, 19, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900588789 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 Building ZINC000900588789 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900588789 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 198) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1) `ZINC000900588789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900588789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900588789 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 14, 14, 14, 25, 25, 25, 14, 14, 14, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 199) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1) `ZINC000900588789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900588789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900588789 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)(C)C)nn1c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 12, 12, 12, 22, 22, 22, 12, 12, 12, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 19, 19, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900588789 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900588789 Building ZINC000900608048 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900608048 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/200 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1) `ZINC000900608048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900608048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900608048 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/201 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1) `ZINC000900608048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900608048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900608048 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900608048 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 Building ZINC000900608048 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900608048 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 200) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1) `ZINC000900608048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900608048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900608048 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 201) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1) `ZINC000900608048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900608048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900608048 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(C(C)(C)c2ccccc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900608048 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900608048 Building ZINC000900615292 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900615292 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/202 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1) `ZINC000900615292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900615292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615292 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 6, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 6, 17, 17, 19, 19, 19, 19, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/203 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1) `ZINC000900615292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900615292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615292 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 18, 18, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900615292 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 Building ZINC000900615292 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900615292 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 202) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1) `ZINC000900615292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900615292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615292 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 6, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 6, 17, 17, 19, 19, 19, 19, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 203) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1) `ZINC000900615292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900615292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615292 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 18, 18, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 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, 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/132203/xbs-8058115.45/working/building/ZINC000900615292 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900615292 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615292 Building ZINC000900615293 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900615293 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/204 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1) `ZINC000900615293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900615293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615293 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 17, 17, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/205 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1) `ZINC000900615293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900615293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615293 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 6, 6, 6, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 6, 19, 19, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900615293 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 Building ZINC000900615293 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900615293 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 204) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1) `ZINC000900615293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900615293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615293 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 17, 17, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 37] set([0, 1, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 205) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1) `ZINC000900615293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900615293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900615293 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)C[C@@H]1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 7, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 6, 6, 6, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 6, 19, 19, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900615293 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900615293 Building ZINC000900628369 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900628369 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/206 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1) `ZINC000900628369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900628369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900628369 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 8, 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, 9, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/207 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1) `ZINC000900628369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900628369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900628369 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 8, 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, 9, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900628369 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 Building ZINC000900628369 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900628369 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 206) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1) `ZINC000900628369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900628369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900628369 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 8, 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, 9, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 207) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1) `ZINC000900628369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900628369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900628369 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ccc3c(c2)CCO3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 8, 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, 9, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900628369 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900628369 Building ZINC000900632018 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900632018 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/208 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1) `ZINC000900632018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900632018 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/209 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1) `ZINC000900632018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900632018 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900632018 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 Building ZINC000900632018 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900632018 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 208) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1) `ZINC000900632018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900632018 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 209) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1) `ZINC000900632018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900632018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900632018 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc3c(c2)CCO3)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900632018 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900632018 Building ZINC000900637024 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900637024 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/210 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1) `ZINC000900637024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900637024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900637024 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/211 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1) `ZINC000900637024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900637024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900637024 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900637024 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 Building ZINC000900637024 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900637024 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 210) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1) `ZINC000900637024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900637024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900637024 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 211) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1) `ZINC000900637024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900637024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900637024 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2sc(C)nc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900637024 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900637024 Building ZINC000900633515 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900633515 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/212 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1) `ZINC000900633515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900633515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900633515 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 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, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 18, 18, 16, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/213 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1) `ZINC000900633515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900633515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900633515 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 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, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 18, 18, 13, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900633515 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 Building ZINC000900633515 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900633515 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 212) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1) `ZINC000900633515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900633515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900633515 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 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, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 18, 18, 16, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 213) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1) `ZINC000900633515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900633515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900633515 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccccc2OC)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 14, 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, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 18, 18, 13, 18, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900633515 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900633515 Building ZINC000900649607 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900649607 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/214 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1) `ZINC000900649607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900649607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900649607 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/215 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1) `ZINC000900649607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900649607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900649607 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 8, 15, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900649607 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 Building ZINC000900649607 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900649607 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 214) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1) `ZINC000900649607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900649607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900649607 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 215) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1) `ZINC000900649607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900649607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000900649607 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CNC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 8, 15, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900649607 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900649607 Building ZINC000900659536 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900659536 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/216 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1) `ZINC000900659536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900659536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900659536 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/217 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1) `ZINC000900659536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900659536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900659536 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 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]) total number of confs: 55 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900659536 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 Building ZINC000900659536 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900659536 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 216) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1) `ZINC000900659536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900659536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900659536 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 217) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1) `ZINC000900659536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900659536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900659536 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(NC(=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 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]) total number of confs: 55 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900659536 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900659536 Building ZINC000900666290 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900666290 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/218 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1) `ZINC000900666290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900666290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900666290 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 22, 22, 22, 22, 13] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/219 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1) `ZINC000900666290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900666290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900666290 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 22, 22, 22, 22, 13] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900666290 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 Building ZINC000900666290 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900666290 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 218) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1) `ZINC000900666290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900666290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900666290 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 22, 22, 22, 22, 13] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 219) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1) `ZINC000900666290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900666290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900666290 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 22, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 22, 22, 22, 22, 13] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900666290 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900666290 Building ZINC000900671540 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900671540 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/220 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C) `ZINC000900671540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900671540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900671540 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 19, 19, 19, 20, 20, 20, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/221 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C) `ZINC000900671540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900671540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900671540 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900671540 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 Building ZINC000900671540 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900671540 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 220) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C) `ZINC000900671540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900671540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900671540 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 19, 19, 19, 20, 20, 20, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 221) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C) `ZINC000900671540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900671540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000900671540 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)C(C)(C)C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900671540 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900671540 Building ZINC000900708050 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900708050 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/222 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F) `ZINC000900708050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900708050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900708050 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 6, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/223 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F) `ZINC000900708050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900708050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900708050 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 6, 14, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900708050 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 Building ZINC000900708050 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900708050 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 222) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F) `ZINC000900708050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900708050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900708050 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 6, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 223) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F) `ZINC000900708050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900708050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000900708050 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 6, 14, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900708050 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708050 Building ZINC000900708269 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900708269 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/224 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1) `ZINC000900708269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900708269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900708269 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/225 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1) `ZINC000900708269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900708269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900708269 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 12, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900708269 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 Building ZINC000900708269 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900708269 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 224) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1) `ZINC000900708269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900708269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900708269 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 225) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1) `ZINC000900708269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900708269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900708269 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(Cl)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 12, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900708269 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900708269 Building ZINC000900726609 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900726609 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/226 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl) `ZINC000900726609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900726609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900726609 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 11, 20, 20, 13, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 11, 20, 20, 14, 20] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/227 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl) `ZINC000900726609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900726609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900726609 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 10, 19, 19, 12, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 10, 10, 19, 19, 13, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900726609 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 Building ZINC000900726609 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900726609 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 226) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl) `ZINC000900726609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900726609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900726609 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 11, 20, 20, 13, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 11, 11, 20, 20, 14, 20] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 227) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl) `ZINC000900726609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900726609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900726609 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nccn1Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 10, 19, 19, 12, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 10, 10, 19, 19, 13, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900726609 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900726609 Building ZINC000900727522 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900727522 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/228 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1) `ZINC000900727522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900727522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900727522 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 12, 1, 12, 12, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18] 46 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]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/229 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1) `ZINC000900727522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900727522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900727522 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 12, 1, 12, 12, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 7, 18, 18, 18, 18, 12, 18, 18, 18, 18] 46 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]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900727522 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 Building ZINC000900727522 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900727522 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 228) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1) `ZINC000900727522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900727522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900727522 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 12, 1, 12, 12, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18] 46 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]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 229) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1) `ZINC000900727522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900727522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900727522 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(C)cc(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 12, 1, 12, 12, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 7, 18, 18, 18, 18, 12, 18, 18, 18, 18] 46 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]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900727522 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900727522 Building ZINC000900730297 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900730297 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/230 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1) `ZINC000900730297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900730297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730297 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 2, 11, 11, 16, 19, 19, 19, 19, 19, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 3, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/231 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1) `ZINC000900730297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900730297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730297 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 2, 9, 9, 16, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 7, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900730297 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 Building ZINC000900730297 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900730297 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 230) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1) `ZINC000900730297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900730297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730297 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 2, 11, 11, 16, 19, 19, 19, 19, 19, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 3, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 231) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1) `ZINC000900730297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900730297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730297 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 2, 9, 9, 16, 19, 19, 19, 19, 19, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 7, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900730297 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730297 Building ZINC000900730298 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900730298 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/232 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1) `ZINC000900730298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900730298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730298 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 2, 10, 10, 16, 19, 19, 19, 19, 19, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 3, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/233 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1) `ZINC000900730298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900730298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730298 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 2, 10, 10, 15, 20, 20, 20, 20, 20, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 2, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900730298 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 Building ZINC000900730298 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900730298 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 232) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1) `ZINC000900730298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900730298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730298 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 2, 10, 10, 16, 19, 19, 19, 19, 19, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 3, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 233) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1) `ZINC000900730298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900730298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000900730298 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 10, 10, 2, 10, 10, 15, 20, 20, 20, 20, 20, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 2, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900730298 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900730298 Building ZINC000900785424 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785424 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/234 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/235 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/236 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/236' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/237 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/237' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785424 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 Building ZINC000900785424 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785424 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 234) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 235) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 236) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 237) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785424 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 Building ZINC000900785424 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785424 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 234) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 235) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 236) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 237) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785424 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 Building ZINC000900785424 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785424 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 234) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 235) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 236) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 237) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785424 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785424 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785424 Building ZINC000900785428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/238 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/239 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/240 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/241 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 Building ZINC000900785428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 238) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 239) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 240) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 241) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 Building ZINC000900785428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 238) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 239) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 240) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 241) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 Building ZINC000900785428 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785428 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 238) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 239) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 240) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 5, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13] 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]) total number of confs: 65 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 241) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785428.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785428 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785428 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785428 Building ZINC000900785430 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785430 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/242 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/243 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/244 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/244' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/245 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/245' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785430 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 Building ZINC000900785430 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785430 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 242) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 243) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 244) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 245) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785430 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 Building ZINC000900785430 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785430 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 242) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 243) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 244) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 245) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785430 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 Building ZINC000900785430 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785430 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 242) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 243) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 244) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 245) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1) `ZINC000900785430.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785430 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCN(Cc2ccccc2)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 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]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785430 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785430 Building ZINC000900785431 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785431 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/246 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/247 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/248 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/248' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/249 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/249' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785431 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 Building ZINC000900785431 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785431 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 246) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 247) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 248) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 249) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785431 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 Building ZINC000900785431 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785431 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 246) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 247) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 248) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 249) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785431 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 Building ZINC000900785431 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000900785431 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 246) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 247) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 248) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12] 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]) total number of confs: 70 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 249) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1) `ZINC000900785431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000900785431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000900785431 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCN(Cc2ccccc2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 12, 12, 12, 12, 12, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 18, 18, 19, 19, 18, 19, 19, 12, 12, 12, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900785431 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900785431 Building ZINC000900793550 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900793550 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/250 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1) `ZINC000900793550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900793550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900793550 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 7, 11, 11, 11, 11, 4, 11, 11, 11, 11, 13, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 11, 13, 13, 13, 11] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/251 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1) `ZINC000900793550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900793550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900793550 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 6, 9, 9, 9, 9, 4, 10, 10, 10, 10, 12, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 10, 10, 12, 12, 12, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900793550 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 Building ZINC000900793550 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900793550 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 250) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1) `ZINC000900793550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900793550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900793550 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 7, 11, 11, 11, 11, 4, 11, 11, 11, 11, 13, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 11, 13, 13, 13, 11] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 251) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1) `ZINC000900793550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900793550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900793550 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)c1ccc(OC)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 6, 9, 9, 9, 9, 4, 10, 10, 10, 10, 12, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 10, 10, 12, 12, 12, 10] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900793550 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900793550 Building ZINC000900812465 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900812465 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/252 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1) `ZINC000900812465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900812465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900812465 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 10, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/253 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1) `ZINC000900812465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900812465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900812465 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 10, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900812465 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 Building ZINC000900812465 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900812465 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 252) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1) `ZINC000900812465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900812465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900812465 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 10, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 253) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1) `ZINC000900812465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900812465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000900812465 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(OCC2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 10, 17, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900812465 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900812465 Building ZINC000900826213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900826213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/254 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1) `ZINC000900826213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900826213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900826213 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/255 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1) `ZINC000900826213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900826213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900826213 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900826213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 Building ZINC000900826213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900826213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 254) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1) `ZINC000900826213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900826213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900826213 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 255) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1) `ZINC000900826213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900826213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900826213 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C)nn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900826213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900826213 Building ZINC000900828651 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900828651 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/256 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1) `ZINC000900828651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900828651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900828651 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 15, 17, 17, 15, 16, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/257 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1) `ZINC000900828651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900828651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900828651 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 15, 17, 17, 15, 15, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900828651 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 Building ZINC000900828651 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900828651 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 256) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1) `ZINC000900828651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900828651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900828651 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 15, 17, 17, 15, 16, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 257) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1) `ZINC000900828651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900828651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000900828651 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(OC)cc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 15, 17, 17, 15, 15, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900828651 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900828651 Building ZINC000900851689 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900851689 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/258 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F) `ZINC000900851689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900851689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900851689 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 15, 16, 16, 15, 16, 16, 16, 6, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 16, 16, 16, 16, 10, 10] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/259 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F) `ZINC000900851689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900851689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900851689 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 15, 16, 16, 15, 16, 16, 16, 6, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 16, 16, 16, 16, 9, 9] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900851689 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 Building ZINC000900851689 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900851689 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 258) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F) `ZINC000900851689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900851689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900851689 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 15, 16, 16, 15, 16, 16, 16, 6, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 16, 16, 16, 16, 10, 10] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 259) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F) `ZINC000900851689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900851689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000900851689 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 15, 16, 16, 15, 16, 16, 16, 6, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 16, 16, 16, 16, 9, 9] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900851689 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900851689 Building ZINC000900876524 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900876524 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/260 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1) `ZINC000900876524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900876524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900876524 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/261 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1) `ZINC000900876524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900876524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900876524 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900876524 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 Building ZINC000900876524 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900876524 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 260) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1) `ZINC000900876524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900876524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900876524 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 261) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1) `ZINC000900876524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900876524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000900876524 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 18, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900876524 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900876524 Building ZINC000900884477 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900884477 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/262 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1) `ZINC000900884477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900884477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900884477 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/263 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1) `ZINC000900884477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900884477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900884477 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900884477 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 Building ZINC000900884477 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900884477 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 262) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1) `ZINC000900884477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900884477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900884477 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 263) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1) `ZINC000900884477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900884477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900884477 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(CC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900884477 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900884477 Building ZINC000900908230 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900908230 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/264 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C) `ZINC000900908230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900908230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900908230 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 10, 10, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/265 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C) `ZINC000900908230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900908230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900908230 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 6, 10, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 4, 6, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900908230 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 Building ZINC000900908230 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900908230 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 264) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C) `ZINC000900908230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900908230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900908230 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 10, 10, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 265) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C) `ZINC000900908230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900908230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000900908230 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1CC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 6, 10, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 4, 6, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900908230 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900908230 Building ZINC000900911162 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900911162 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/266 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900911162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911162 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/267 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900911162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911162 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900911162 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 Building ZINC000900911162 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900911162 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 266) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900911162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911162 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 267) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900911162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911162 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900911162 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911162 Building ZINC000900911163 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900911163 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/268 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900911163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911163 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/269 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900911163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911163 none CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900911163 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 Building ZINC000900911163 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900911163 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 268) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900911163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911163 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 269) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1) `ZINC000900911163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900911163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000900911163 none CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1nc(C(F)(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900911163 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900911163 Building ZINC000900928559 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900928559 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/270 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1) `ZINC000900928559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900928559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900928559 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 11, 14, 18, 18, 18, 18, 18, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 14, 14, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/271 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1) `ZINC000900928559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900928559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900928559 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 11, 12, 17, 17, 17, 17, 17, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 12, 12, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900928559 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 Building ZINC000900928559 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900928559 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 270) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1) `ZINC000900928559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900928559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900928559 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 11, 14, 18, 18, 18, 18, 18, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 14, 14, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 271) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1) `ZINC000900928559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900928559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900928559 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCc2ccccn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 11, 12, 17, 17, 17, 17, 17, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 12, 12, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900928559 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900928559 Building ZINC000900977036 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900977036 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/272 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900977036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977036 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 23, 24, 24, 23, 23, 24, 24, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 24, 24, 24, 24] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/273 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900977036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977036 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 21, 21, 21, 21, 23, 23, 23, 23, 23, 23, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 23, 23, 23, 23] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900977036 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 Building ZINC000900977036 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900977036 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 272) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900977036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977036 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 23, 24, 24, 23, 23, 24, 24, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 24, 24, 24, 24] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 273) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900977036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977036 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 21, 21, 21, 21, 23, 23, 23, 23, 23, 23, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 23, 23, 23, 23] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900977036 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977036 Building ZINC000900977039 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900977039 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/274 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900977039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977039 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 19, 19, 19, 19, 21, 21, 21, 21, 21, 21, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 21, 21, 21, 21] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/275 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900977039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977039 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 23, 24, 24, 23, 23, 24, 24, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 24, 24, 24, 24] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900977039 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 Building ZINC000900977039 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900977039 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 274) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900977039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977039 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 19, 19, 19, 19, 21, 21, 21, 21, 21, 21, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 21, 21, 21, 21] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 275) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1) `ZINC000900977039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900977039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000900977039 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C)c1noc(c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 23, 24, 24, 23, 23, 24, 24, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 24, 24, 24, 24] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900977039 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900977039 Building ZINC000900978846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900978846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/276 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)n1) `ZINC000900978846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900978846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000900978846 none CCc1noc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 12, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/277 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)n1) `ZINC000900978846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900978846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000900978846 none CCc1noc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 13, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900978846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 Building ZINC000900978846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900978846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 276) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)n1) `ZINC000900978846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900978846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000900978846 none CCc1noc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 12, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 277) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)n1) `ZINC000900978846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900978846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000900978846 none CCc1noc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 1, 8, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 13, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900978846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900978846 Building ZINC000900999966 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900999966 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/278 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1) `ZINC000900999966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900999966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900999966 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 19, 19, 19, 19, 19, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/279 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1) `ZINC000900999966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900999966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900999966 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900999966 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 Building ZINC000900999966 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000900999966 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 278) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1) `ZINC000900999966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000900999966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900999966 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 11, 19, 19, 19, 19, 19, 19, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 19, 19, 19, 19, 19, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 279) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1) `ZINC000900999966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000900999966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000900999966 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2nccc(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000900999966 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000900999966 Building ZINC000901005278 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901005278 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/280 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1) `ZINC000901005278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901005278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901005278 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 18, 18, 18, 18, 18, 22, 22, 18, 21, 22, 22, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 18, 18, 18, 22, 22, 22, 22] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/281 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1) `ZINC000901005278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901005278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901005278 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 18, 18, 18, 18, 18, 22, 22, 20, 20, 22, 22, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 18, 18, 18, 22, 22, 22, 22] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901005278 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 Building ZINC000901005278 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901005278 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 280) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1) `ZINC000901005278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901005278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901005278 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 18, 18, 18, 18, 18, 22, 22, 18, 21, 22, 22, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 18, 18, 18, 22, 22, 22, 22] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 281) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1) `ZINC000901005278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901005278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901005278 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1nc(C)c(c2ccc(Cl)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 12, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 5, 18, 18, 18, 18, 18, 22, 22, 20, 20, 22, 22, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 18, 18, 18, 22, 22, 22, 22] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901005278 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901005278 Building ZINC000901013470 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901013470 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/282 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1) `ZINC000901013470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901013470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901013470 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 19, 19, 15, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 19, 19, 19, 19, 19, 6] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/283 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1) `ZINC000901013470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901013470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901013470 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 18, 18, 15, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901013470 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 Building ZINC000901013470 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901013470 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 282) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1) `ZINC000901013470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901013470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901013470 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 19, 19, 15, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 19, 19, 19, 19, 19, 6] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 283) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1) `ZINC000901013470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901013470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000901013470 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2noc(C3CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 15, 15, 15, 15, 18, 18, 15, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 18, 18, 18, 18, 18, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901013470 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901013470 Building ZINC000901019056 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901019056 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/284 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1) `ZINC000901019056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901019056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901019056 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 10, 10, 10, 10, 10] 30 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/285 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1) `ZINC000901019056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901019056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901019056 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 10, 10, 10, 10, 10] 29 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]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901019056 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 Building ZINC000901019056 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901019056 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 284) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1) `ZINC000901019056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901019056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901019056 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 10, 10, 10, 10, 10] 30 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 285) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1) `ZINC000901019056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901019056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901019056 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2cccc(Br)c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 6, 10, 10, 10, 10, 10] 29 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]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901019056 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901019056 Building ZINC000901051258 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901051258 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/286 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1) `ZINC000901051258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901051258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901051258 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 34] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/287 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1) `ZINC000901051258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901051258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901051258 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 34] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901051258 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 Building ZINC000901051258 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901051258 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 286) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1) `ZINC000901051258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901051258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901051258 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 34] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 287) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1) `ZINC000901051258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901051258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901051258 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(OC(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 10, 11, 34] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901051258 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901051258 Building ZINC000901082334 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901082334 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/288 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1) `ZINC000901082334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901082334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082334 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/289 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1) `ZINC000901082334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901082334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082334 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901082334 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 Building ZINC000901082334 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901082334 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 288) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1) `ZINC000901082334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901082334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082334 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 289) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1) `ZINC000901082334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901082334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082334 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901082334 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082334 Building ZINC000901082335 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901082335 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/290 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1) `ZINC000901082335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901082335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082335 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/291 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1) `ZINC000901082335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901082335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082335 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901082335 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 Building ZINC000901082335 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901082335 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 290) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1) `ZINC000901082335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901082335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082335 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 291) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1) `ZINC000901082335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901082335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000901082335 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901082335 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901082335 Building ZINC000901108259 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901108259 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/292 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1) `ZINC000901108259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901108259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901108259 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 15, 15, 10, 14, 15, 15, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 15, 15, 15, 15] 35 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]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/293 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1) `ZINC000901108259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901108259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901108259 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 15, 15, 14, 15, 15, 15, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 15, 15, 15, 15] 35 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]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901108259 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 Building ZINC000901108259 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901108259 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 292) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1) `ZINC000901108259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901108259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901108259 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 15, 15, 10, 14, 15, 15, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 15, 15, 15, 15] 35 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]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 293) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1) `ZINC000901108259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901108259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000901108259 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2ccc(Cl)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 15, 15, 14, 15, 15, 15, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 6, 15, 15, 15, 15] 35 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]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901108259 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901108259 Building ZINC000901126246 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901126246 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/294 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1) `ZINC000901126246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901126246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901126246 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 5, 9, 14, 14, 14, 14, 5, 8, 10, 10, 9, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 14, 14, 14, 8, 8, 10, 10, 20, 10, 10] 100 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/295 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1) `ZINC000901126246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901126246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901126246 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 5, 9, 14, 14, 14, 14, 5, 8, 10, 10, 8, 8, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 14, 14, 14, 8, 8, 10, 10, 20, 10, 10] 100 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901126246 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 Building ZINC000901126246 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901126246 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 294) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1) `ZINC000901126246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901126246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901126246 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 5, 9, 14, 14, 14, 14, 5, 8, 10, 10, 9, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 14, 14, 14, 8, 8, 10, 10, 20, 10, 10] 100 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 295) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1) `ZINC000901126246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901126246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901126246 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 5, 9, 14, 14, 14, 14, 5, 8, 10, 10, 8, 8, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 14, 14, 14, 8, 8, 10, 10, 20, 10, 10] 100 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901126246 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901126246 Building ZINC000901145081 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901145081 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/296 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)C(C)C) `ZINC000901145081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901145081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000901145081 none CCCN(C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 4, 10, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15] 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: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/297 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)C(C)C) `ZINC000901145081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901145081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000901145081 none CCCN(C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 4, 10, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15] 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: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901145081 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 Building ZINC000901145081 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901145081 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 296) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)C(C)C) `ZINC000901145081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901145081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000901145081 none CCCN(C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 4, 10, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15] 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: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 297) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)C(C)C) `ZINC000901145081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901145081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000901145081 none CCCN(C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 4, 10, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15] 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: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901145081 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901145081 Building ZINC000901178363 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901178363 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/298 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901178363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178363 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/299 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901178363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178363 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 8, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9] 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901178363 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 Building ZINC000901178363 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901178363 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 298) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901178363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178363 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 299) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901178363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178363 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 8, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 9, 9] 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901178363 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178363 Building ZINC000901178364 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901178364 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/300 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901178364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178364 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/301 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901178364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178364 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901178364 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 Building ZINC000901178364 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901178364 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 300) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901178364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178364 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 301) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1) `ZINC000901178364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901178364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000901178364 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2nc3ccc(C)cc3[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901178364 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901178364 Building ZINC000901174709 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901174709 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/302 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21) `ZINC000901174709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901174709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901174709 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 8, 8, 8, 8] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/303 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21) `ZINC000901174709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901174709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901174709 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 8, 8, 8, 8] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901174709 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 Building ZINC000901174709 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901174709 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 302) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21) `ZINC000901174709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901174709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901174709 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 8, 8, 8, 8] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 303) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21) `ZINC000901174709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901174709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000901174709 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccco2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 8, 8, 8, 8] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901174709 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901174709 Building ZINC000913166369 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913166369 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/304 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1) `ZINC000913166369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913166369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913166369 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 42 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]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/305 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1) `ZINC000913166369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913166369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913166369 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12] 41 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]) total number of confs: 57 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913166369 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 Building ZINC000913166369 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913166369 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 304) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1) `ZINC000913166369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913166369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913166369 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 42 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]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 305) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1) `ZINC000913166369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913166369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913166369 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cccc(C(F)(F)F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12] 41 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]) total number of confs: 57 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913166369 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913166369 Building ZINC000901196933 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901196933 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/306 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1) `ZINC000901196933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901196933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901196933 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 3, 12, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/307 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1) `ZINC000901196933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901196933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901196933 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 14, 17, 17, 14, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901196933 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 Building ZINC000901196933 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901196933 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 306) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1) `ZINC000901196933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901196933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901196933 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 3, 12, 17, 17, 12, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 307) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1) `ZINC000901196933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901196933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901196933 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 14, 17, 17, 14, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901196933 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901196933 Building ZINC000901228815 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901228815 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/308 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O) `ZINC000901228815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901228815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000901228815 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 19, 19, 19, 15, 19, 19, 19, 19, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 19, 19, 38] 100 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]) total number of confs: 121 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/309 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O) `ZINC000901228815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901228815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000901228815 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 19, 19, 38] 100 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]) total number of confs: 101 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901228815 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 Building ZINC000901228815 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901228815 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 308) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O) `ZINC000901228815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901228815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000901228815 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 19, 19, 19, 15, 19, 19, 19, 19, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 19, 19, 38] 100 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]) total number of confs: 121 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 309) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O) `ZINC000901228815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901228815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000901228815 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 19, 19, 38] 100 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]) total number of confs: 101 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901228815 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901228815 Building ZINC000901239199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901239199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/310 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C) `ZINC000901239199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901239199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000901239199 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 58 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/311 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C) `ZINC000901239199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901239199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000901239199 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 58 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901239199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 Building ZINC000901239199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901239199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 310) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C) `ZINC000901239199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901239199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000901239199 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 58 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 311) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C) `ZINC000901239199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901239199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000901239199 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(C)(C)C)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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]) total number of confs: 58 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901239199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901239199 Building ZINC000901343568 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901343568 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/312 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1) `ZINC000901343568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901343568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000901343568 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 22, 22, 22, 22, 12] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/313 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1) `ZINC000901343568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901343568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000901343568 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 22, 22, 22, 22, 12] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901343568 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 Building ZINC000901343568 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000901343568 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 312) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1) `ZINC000901343568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901343568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000901343568 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 22, 22, 22, 22, 12] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 313) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1) `ZINC000901343568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000901343568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000901343568 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3ccccn3)oc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 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, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 22, 22, 22, 22, 12] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901343568 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901343568 Building ZINC000184593286 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184593286 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/314 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(C(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000184593286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184593286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000184593286 none O=C(NCc1ccc(C(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 12, 12, 32, 33, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 23, 23, 32, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/315 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(C(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000184593286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184593286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000184593286 none O=C(NCc1ccc(C(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 12, 12, 30, 30, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 23, 23, 30, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000184593286 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 Building ZINC000184593286 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184593286 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 314) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCc1ccc(C(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000184593286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184593286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000184593286 none O=C(NCc1ccc(C(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 12, 12, 32, 33, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 23, 23, 32, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 315) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCc1ccc(C(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000184593286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184593286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000184593286 none O=C(NCc1ccc(C(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 12, 12, 30, 30, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 23, 23, 30, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000184593286 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000184593286 Building ZINC000146633370 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633370 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/316 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633370 none O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/317 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633370 none O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633370 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 Building ZINC000146633370 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633370 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 316) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633370 none O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 317) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633370 none O=C(N[C@@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633370 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633370 Building ZINC000146633575 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633575 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/318 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633575 none O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/319 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633575 none O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633575 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 Building ZINC000146633575 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633575 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 318) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633575 none O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 319) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633575 none O=C(N[C@H]1CCC[C@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633575 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633575 Building ZINC000146633793 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633793 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/320 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633793 none O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/321 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633793 none O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633793 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 Building ZINC000146633793 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633793 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 320) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633793 none O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 321) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633793 none O=C(N[C@@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633793 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633793 Building ZINC000146633970 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633970 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/322 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633970 none O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/323 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633970 none O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633970 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 Building ZINC000146633970 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000146633970 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 322) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000146633970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633970 none O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 323) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000146633970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000146633970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000146633970 none O=C(N[C@H]1CCC[C@@H](C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000146633970 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000146633970 Building ZINC000153242965 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153242965 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/324 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153242965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153242965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153242965 none COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 7, 7] 27 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]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/325 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153242965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153242965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153242965 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 8, 8] 27 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000153242965 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 Building ZINC000153242965 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153242965 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 324) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153242965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153242965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153242965 none COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 7, 7] 27 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]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 325) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153242965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153242965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153242965 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 21, 21, 14, 21, 21, 14, 14, 14, 8, 8] 27 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000153242965 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153242965 Building ZINC000153243192 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153243192 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/326 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153243192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153243192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153243192 none COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 10, 10, 5, 5] 25 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]) total number of confs: 77 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/327 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153243192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153243192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153243192 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 33, 33, 15, 33, 33, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 33, 33, 15, 33, 33, 15, 15, 15, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000153243192 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 Building ZINC000153243192 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000153243192 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 326) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153243192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000153243192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153243192 none COc1ccc([C@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 10, 10, 5, 5] 25 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]) total number of confs: 77 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 327) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)cc1) `ZINC000153243192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000153243192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000153243192 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2[C@H](C)C[C@@H](c3ccccc3)[C@@H]2C)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 33, 33, 15, 33, 33, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 33, 33, 15, 33, 33, 15, 15, 15, 10, 10] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000153243192 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000153243192 Building ZINC000156095003 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156095003 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/328 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)cc1) `ZINC000156095003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000156095003 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 41, 41, 41, 11, 41, 41, 41, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 11, 11, 41, 41, 41, 41, 11, 41, 41, 41, 41, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/329 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)cc1) `ZINC000156095003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000156095003 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 43, 43, 43, 12, 43, 43, 43, 12, 12, 12, 9, 9, 9, 9, 9, 9, 9, 12, 12, 43, 43, 43, 43, 13, 43, 43, 43, 43, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000156095003 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 Building ZINC000156095003 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156095003 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 328) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)cc1) `ZINC000156095003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000156095003 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 8, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 41, 41, 41, 11, 41, 41, 41, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 11, 11, 41, 41, 41, 41, 11, 41, 41, 41, 41, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 329) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)cc1) `ZINC000156095003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000156095003 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(c3cc(C)cc(C)c3)n[nH]2)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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 8, 6, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 43, 43, 43, 12, 43, 43, 43, 12, 12, 12, 9, 9, 9, 9, 9, 9, 9, 12, 12, 43, 43, 43, 43, 13, 43, 43, 43, 43, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000156095003 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156095003 Building ZINC000156327835 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156327835 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/330 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)cc1) `ZINC000156327835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156327835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000156327835 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 36, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/331 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)cc1) `ZINC000156327835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156327835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000156327835 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 36, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000156327835 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 Building ZINC000156327835 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000156327835 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 330) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)cc1) `ZINC000156327835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000156327835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000156327835 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 36, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 331) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)cc1) `ZINC000156327835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000156327835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000156327835 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(NC3CCCC3)c2)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', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 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, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 36, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000156327835 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000156327835 Building ZINC000633740078 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633740078 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/332 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1) `ZINC000633740078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633740078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000633740078 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1 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.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 13, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/333 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1) `ZINC000633740078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633740078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000633740078 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1 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.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 14, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633740078 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 Building ZINC000633740078 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633740078 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 332) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1) `ZINC000633740078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633740078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000633740078 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1 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.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 13, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 333) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1) `ZINC000633740078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633740078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000633740078 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C2CCCCCC2)cs1 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.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 14, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633740078 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633740078 Building ZINC000633791153 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633791153 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/334 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl) `ZINC000633791153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633791153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/335 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl) `ZINC000633791153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633791153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 4, 4, 4, 10, 10, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633791153 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 Building ZINC000633791153 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633791153 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 334) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl) `ZINC000633791153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633791153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 6, 6, 6, 12, 12, 12, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 335) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl) `ZINC000633791153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633791153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 4, 4, 4, 10, 10, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633791153 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791153 Building ZINC000633791163 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633791163 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/336 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl) `ZINC000633791163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633791163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791163 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 4, 4, 4, 12, 12, 12, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/337 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl) `ZINC000633791163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633791163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791163 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633791163 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 Building ZINC000633791163 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633791163 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 336) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl) `ZINC000633791163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633791163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791163 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 4, 4, 4, 12, 12, 12, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 337) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl) `ZINC000633791163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633791163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000633791163 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)[C@H]2c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 6, 6, 6, 13, 13, 13, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633791163 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633791163 Building ZINC000633843760 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633843760 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/338 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1) `ZINC000633843760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633843760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000633843760 none C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 26, 26, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 12, 12, 6, 12, 12, 17, 17, 17, 26, 26, 26, 26, 26, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/339 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1) `ZINC000633843760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633843760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000633843760 none C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 30, 30, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 10, 14, 14, 10, 14, 14, 21, 21, 21, 30, 30, 30, 30, 30, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 14, 14, 10, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633843760 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 Building ZINC000633843760 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000633843760 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 338) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1) `ZINC000633843760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000633843760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000633843760 none C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 26, 26, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 12, 12, 6, 12, 12, 17, 17, 17, 26, 26, 26, 26, 26, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 339) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1) `ZINC000633843760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000633843760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000633843760 none C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 30, 30, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 10, 14, 14, 10, 14, 14, 21, 21, 21, 30, 30, 30, 30, 30, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 14, 14, 10, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000633843760 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000633843760 Building ZINC000836835680 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000836835680 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/340 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1) `ZINC000836835680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000836835680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000836835680 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 18, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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, 45]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/341 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1) `ZINC000836835680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000836835680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000836835680 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 18, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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, 45]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000836835680 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 Building ZINC000836835680 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000836835680 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 340) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1) `ZINC000836835680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000836835680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000836835680 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 18, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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, 45]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 341) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1) `ZINC000836835680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000836835680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000836835680 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(F)(Cc2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 18, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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, 45]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000836835680 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000836835680 Building ZINC000751991736 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751991736 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/342 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000751991736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751991736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000751991736 none O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/343 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000751991736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751991736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000751991736 none O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000751991736 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 Building ZINC000751991736 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751991736 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 342) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000751991736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751991736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000751991736 none O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 343) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000751991736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751991736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000751991736 none O=C(N1CCc2cc(c3ccccc3)oc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 24, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000751991736 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000751991736 Building ZINC000911860856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911860856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/344 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C) `ZINC000911860856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911860856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000911860856 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 10, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/345 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C) `ZINC000911860856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911860856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000911860856 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911860856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 Building ZINC000911860856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911860856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 344) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C) `ZINC000911860856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911860856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000911860856 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 10, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 345) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C) `ZINC000911860856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911860856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000911860856 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)c1ccccc1N=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911860856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911860856 Building ZINC000753995862 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753995862 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/346 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753995862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753995862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000753995862 none O=C(Nc1ccc(SC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 42, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/347 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753995862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753995862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000753995862 none O=C(Nc1ccc(SC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 42, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000753995862 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 Building ZINC000753995862 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753995862 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 346) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753995862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753995862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000753995862 none O=C(Nc1ccc(SC(F)F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 42, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 347) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753995862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753995862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000753995862 none O=C(Nc1ccc(SC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 42, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000753995862 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753995862 Building ZINC000753997777 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753997777 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/348 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753997777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753997777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000753997777 none O=C(Nc1ccc(N2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 5, 10, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/349 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753997777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753997777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000753997777 none O=C(Nc1ccc(N2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 5, 11, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 13, 13, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000753997777 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 Building ZINC000753997777 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000753997777 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 348) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(N2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753997777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000753997777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000753997777 none O=C(Nc1ccc(N2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 5, 10, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 349) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(N2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000753997777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000753997777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000753997777 none O=C(Nc1ccc(N2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 5, 11, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 13, 13, 49, 50, 50, 50, 50, 50, 50, 50, 50, 49, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000753997777 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000753997777 Building ZINC000754026539 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754026539 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/350 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1SC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754026539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754026539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754026539 none O=C(Nc1ccccc1SC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 10, 18, 18, 18, 36, 50, 50, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 18, 18, 18, 18, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/351 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1SC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754026539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754026539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754026539 none O=C(Nc1ccccc1SC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 10, 18, 18, 18, 32, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 18, 18, 18, 18, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754026539 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 Building ZINC000754026539 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754026539 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 350) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccccc1SC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754026539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754026539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754026539 none O=C(Nc1ccccc1SC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 10, 18, 18, 18, 36, 50, 50, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 18, 18, 18, 18, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 173 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 351) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccccc1SC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754026539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754026539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754026539 none O=C(Nc1ccccc1SC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 18, 10, 18, 18, 18, 32, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 18, 18, 18, 18, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754026539 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754026539 Building ZINC000754038615 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754038615 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/352 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 15, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/353 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 4, 3, 3, 3, 3, 19, 19, 50, 50, 50, 50] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/354 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/354' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 21, 13, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/355 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/355' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 10, 4, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754038615 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 Building ZINC000754038615 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754038615 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 352) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 15, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 353) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 4, 3, 3, 3, 3, 19, 19, 50, 50, 50, 50] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 354) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 21, 13, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 355) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 10, 4, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754038615 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 Building ZINC000754038615 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754038615 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 352) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 15, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 353) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 4, 3, 3, 3, 3, 19, 19, 50, 50, 50, 50] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 354) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 21, 13, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 355) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 10, 4, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754038615 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 Building ZINC000754038615 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754038615 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 352) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 15, 4, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 4, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 353) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 4, 3, 3, 3, 3, 19, 19, 50, 50, 50, 50] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 354) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 21, 13, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 355) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1) `ZINC000754038615.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754038615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000754038615 none C[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 10, 4, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 3, 3, 21, 21, 50, 50, 50, 50] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754038615 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754038615 Building ZINC000754044007 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754044007 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/356 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1) `ZINC000754044007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754044007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754044007 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 39, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 7, 6, 6, 6, 6, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/357 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1) `ZINC000754044007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754044007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754044007 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 2, 6, 6, 40, 40, 8, 10, 49, 49, 49, 49, 40, 40, 40, 40, 8, 6, 6, 6, 6, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754044007 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 Building ZINC000754044007 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754044007 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 356) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1) `ZINC000754044007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754044007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754044007 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 39, 39, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 7, 6, 6, 6, 6, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 357) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1) `ZINC000754044007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754044007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754044007 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 2, 6, 6, 40, 40, 8, 10, 49, 49, 49, 49, 40, 40, 40, 40, 8, 6, 6, 6, 6, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49] 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]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754044007 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044007 Building ZINC000754044081 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754044081 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/358 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(C2CCCCC2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754044081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754044081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000754044081 none O=C(Nc1nnc(C2CCCCC2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 50, 50, 50, 50, 50, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/359 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(C2CCCCC2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754044081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754044081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000754044081 none O=C(Nc1nnc(C2CCCCC2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 50, 50, 50, 50, 50, 8, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754044081 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 Building ZINC000754044081 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754044081 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 358) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nnc(C2CCCCC2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754044081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754044081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000754044081 none O=C(Nc1nnc(C2CCCCC2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 50, 50, 50, 50, 50, 8, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 359) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nnc(C2CCCCC2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754044081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754044081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000754044081 none O=C(Nc1nnc(C2CCCCC2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 50, 50, 50, 50, 50, 8, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754044081 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754044081 Building ZINC000839693123 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839693123 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/360 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839693123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693123 none CC[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 18, 18, 18, 18, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/361 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839693123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693123 none CC[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 21, 21, 17, 1, 17, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839693123 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 Building ZINC000839693123 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839693123 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 360) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839693123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693123 none CC[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 18, 18, 18, 18, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 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]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 361) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839693123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693123 none CC[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 21, 21, 21, 21, 17, 1, 17, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839693123 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693123 Building ZINC000839693124 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839693124 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/362 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839693124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693124 none CC[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 20, 20, 20, 20, 20, 20, 20, 18, 1, 18, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9] 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]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/363 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839693124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693124 none CC[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 18, 18, 18, 18, 16, 1, 16, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839693124 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 Building ZINC000839693124 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839693124 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 362) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839693124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693124 none CC[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 20, 20, 20, 20, 20, 20, 20, 18, 1, 18, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9] 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]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 363) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839693124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839693124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839693124 none CC[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 18, 18, 18, 18, 16, 1, 16, 1, 1, 1, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839693124 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839693124 Building ZINC000754140352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754140352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/364 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/365 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/366 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/366' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/367 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/367' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754140352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 Building ZINC000754140352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754140352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 364) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 365) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 366) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 367) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754140352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 Building ZINC000754140352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754140352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 364) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 365) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 366) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 367) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754140352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 Building ZINC000754140352 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000754140352 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 364) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 365) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 366) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 367) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000754140352.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000754140352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000754140352 none CC(C)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 23, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 4, 5, 5, 5, 5, 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]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754140352 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754140352 Building ZINC000839734973 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734973 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/368 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734973 none C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 17, 17] 36 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/369 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734973 none C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 17, 17] 38 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734973 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 Building ZINC000839734973 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734973 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 368) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734973 none C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 17, 17] 36 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 369) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734973 none C[C@@H]1C[C@@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 17, 17] 38 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734973 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734973 Building ZINC000839734974 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734974 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/370 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734974 none C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 2, 17, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 25, 25] 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]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/371 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734974 none C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 2, 17, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 24, 24] 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]) total number of confs: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734974 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 Building ZINC000839734974 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734974 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 370) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734974 none C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 2, 17, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 25, 25] 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]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 371) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734974 none C[C@@H]1C[C@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 2, 17, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 24, 24] 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]) total number of confs: 60 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734974 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734974 Building ZINC000839734975 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734975 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/372 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734975 none C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 23, 23] 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/373 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734975 none C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 23, 23] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734975 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 Building ZINC000839734975 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734975 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 372) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734975 none C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 23, 23] 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 373) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734975 none C[C@@H]1C[C@@H](C)[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 23, 23] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734975 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734975 Building ZINC000839734976 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734976 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/374 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734976 none C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 16, 16] 34 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]) total number of confs: 37 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/375 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734976 none C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 18, 18] 37 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734976 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 Building ZINC000839734976 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839734976 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 374) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839734976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734976 none C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 16, 16] 34 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]) total number of confs: 37 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 375) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839734976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839734976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839734976 none C[C@@H]1C[C@H](C)[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 18, 18] 37 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839734976 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839734976 Building ZINC000754147175 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754147175 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/376 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754147175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754147175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754147175 none O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 8, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 23, 31, 41, 41, 41, 41, 31, 31, 31, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 31, 41, 41, 41, 41, 41, 41, 41, 41, 31, 6, 6, 6, 6] 41 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/377 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754147175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754147175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754147175 none O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 8, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 27, 27, 36, 36, 36, 36, 27, 27, 27, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 27, 36, 36, 36, 36, 36, 36, 36, 36, 27, 6, 6, 6, 6] 38 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754147175 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 Building ZINC000754147175 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754147175 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 376) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754147175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754147175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754147175 none O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 8, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 31, 31, 31, 23, 31, 41, 41, 41, 41, 31, 31, 31, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 31, 41, 41, 41, 41, 41, 41, 41, 41, 31, 6, 6, 6, 6] 41 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 377) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754147175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754147175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754147175 none O=C(Nc1cc(F)c(N2CCCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 8, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 27, 27, 27, 27, 27, 36, 36, 36, 36, 27, 27, 27, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 27, 36, 36, 36, 36, 36, 36, 36, 36, 27, 6, 6, 6, 6] 38 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754147175 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754147175 Building ZINC000839739213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839739213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/378 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC2(CC2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839739213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839739213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839739213 none O=C(NC1CCC2(CC2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/379 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCC2(CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839739213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839739213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839739213 none O=C(NC1CCC2(CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839739213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 Building ZINC000839739213 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839739213 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 378) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1CCC2(CC2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839739213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839739213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839739213 none O=C(NC1CCC2(CC2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 379) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1CCC2(CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839739213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839739213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839739213 none O=C(NC1CCC2(CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839739213 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839739213 Building ZINC000754171892 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754171892 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/380 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754171892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754171892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754171892 none O=C(Nc1cccc(N2CCCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/381 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754171892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754171892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754171892 none O=C(Nc1cccc(N2CCCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754171892 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 Building ZINC000754171892 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754171892 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 380) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc(N2CCCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754171892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754171892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754171892 none O=C(Nc1cccc(N2CCCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 381) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc(N2CCCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754171892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754171892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000754171892 none O=C(Nc1cccc(N2CCCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754171892 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754171892 Building ZINC000839783128 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839783128 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/382 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC12CCC(CC1)CC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839783128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839783128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839783128 none O=C(NC12CCC(CC1)CC2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10] 28 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/383 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC12CCC(CC1)CC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839783128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839783128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839783128 none O=C(NC12CCC(CC1)CC2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10] 28 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839783128 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 Building ZINC000839783128 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839783128 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 382) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC12CCC(CC1)CC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839783128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839783128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839783128 none O=C(NC12CCC(CC1)CC2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10] 28 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 383) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC12CCC(CC1)CC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839783128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839783128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000839783128 none O=C(NC12CCC(CC1)CC2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10] 28 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839783128 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839783128 Building ZINC000839789743 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839789743 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/384 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839789743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839789743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839789743 none CC[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 16, 16, 16, 16, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16] 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]) total number of confs: 100 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/385 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839789743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839789743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839789743 none CC[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 14, 14, 14, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 14, 10, 10, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839789743 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 Building ZINC000839789743 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839789743 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 384) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839789743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839789743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839789743 none CC[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 16, 16, 16, 16, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16] 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]) total number of confs: 100 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 385) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC000839789743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839789743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839789743 none CC[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 14, 14, 14, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 14, 10, 10, 14, 14] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839789743 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839789743 Building ZINC000754228573 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754228573 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/386 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(SC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754228573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754228573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754228573 none O=C(Nc1cccc(SC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 43, 50, 50, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 11, 11, 11, 50, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/387 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(SC(F)F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754228573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754228573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754228573 none O=C(Nc1cccc(SC(F)F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 43, 50, 50, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 11, 11, 11, 50, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754228573 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 Building ZINC000754228573 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754228573 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 386) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc(SC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754228573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754228573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754228573 none O=C(Nc1cccc(SC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 43, 50, 50, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 11, 11, 11, 50, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 387) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc(SC(F)F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754228573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754228573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000754228573 none O=C(Nc1cccc(SC(F)F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 43, 50, 50, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 11, 11, 11, 50, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754228573 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754228573 Building ZINC000754247299 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754247299 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/388 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754247299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754247299 none O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 40, 40, 22, 40, 50, 50, 50, 50, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 40, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/389 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754247299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754247299 none O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 37, 37, 25, 37, 49, 49, 49, 49, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 37, 37, 49, 49, 49, 49, 49, 49, 49, 49, 37, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754247299 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 Building ZINC000754247299 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754247299 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 388) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754247299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754247299 none O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 40, 40, 22, 40, 50, 50, 50, 50, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 40, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 389) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754247299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754247299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000754247299 none O=C(Nc1ccc(N2CCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 37, 37, 25, 37, 49, 49, 49, 49, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 37, 37, 49, 49, 49, 49, 49, 49, 49, 49, 37, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754247299 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754247299 Building ZINC000839891189 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839891189 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/390 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)C1) `ZINC000839891189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839891189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839891189 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/391 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)C1) `ZINC000839891189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839891189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839891189 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 10, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839891189 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 Building ZINC000839891189 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839891189 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 390) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)C1) `ZINC000839891189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839891189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839891189 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 9, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 391) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)C1) `ZINC000839891189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839891189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000839891189 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC(C)(C)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.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 10, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000839891189 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000839891189 Building ZINC000840475861 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840475861 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/392 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C2CCC2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000840475861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840475861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000840475861 none O=C(NC1(C2CCC2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 14, 25, 25, 25, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 10, 6, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 83 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/393 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C2CCC2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000840475861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840475861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000840475861 none O=C(NC1(C2CCC2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 14, 27, 27, 27, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 89 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840475861 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 Building ZINC000840475861 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840475861 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 392) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1(C2CCC2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000840475861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840475861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000840475861 none O=C(NC1(C2CCC2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 14, 25, 25, 25, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 10, 6, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 83 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 393) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1(C2CCC2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000840475861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840475861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000840475861 none O=C(NC1(C2CCC2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 14, 27, 27, 27, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 89 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840475861 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840475861 Building ZINC000755108147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000755108147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/394 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000755108147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000755108147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000755108147 none Nc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 25, 25, 25, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 10, 6, 6, 6, 6, 25] 30 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/395 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000755108147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000755108147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000755108147 none Nc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 24, 24, 24, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 9, 6, 6, 6, 6, 24] 29 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000755108147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 Building ZINC000755108147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000755108147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 394) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Nc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000755108147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000755108147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000755108147 none Nc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 25, 25, 25, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 10, 6, 6, 6, 6, 25] 30 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 395) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Nc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000755108147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000755108147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 33 natoms 32 natoms 31 natoms 30 names: ZINC000755108147 none Nc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 24, 24, 24, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 9, 6, 6, 6, 6, 24] 29 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000755108147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755108147 Building ZINC000755143877 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000755143877 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/396 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C) `ZINC000755143877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000755143877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000755143877 none Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/397 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C) `ZINC000755143877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000755143877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000755143877 none Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000755143877 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 Building ZINC000755143877 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000755143877 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 396) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C) `ZINC000755143877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000755143877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000755143877 none Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 397) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C) `ZINC000755143877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000755143877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000755143877 none Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)[nH]c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000755143877 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000755143877 Building ZINC000840927673 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927673 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/398 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927673 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 9, 9, 9, 9, 9, 7, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/399 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927673 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 10, 10, 10, 10, 10, 5, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840927673 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 Building ZINC000840927673 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927673 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 398) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927673 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 9, 9, 9, 9, 9, 7, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 399) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927673 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 10, 10, 10, 10, 10, 5, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840927673 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927673 Building ZINC000840927674 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927674 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/400 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927674 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 10, 10, 10, 10, 10, 6, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/401 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927674 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 2, 9, 9, 9, 9, 9, 7, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840927674 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 Building ZINC000840927674 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927674 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 400) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927674 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 10, 10, 10, 10, 10, 6, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 401) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840927674 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 2, 9, 9, 9, 9, 9, 7, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000840927674 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000840927674 Building ZINC000757724204 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757724204 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/402 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757724204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724204 none O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 1, 2, 5, 5, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/403 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757724204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724204 none O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757724204 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 Building ZINC000757724204 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757724204 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 402) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757724204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724204 none O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 1, 2, 5, 5, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 403) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757724204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724204 none O=C(N[C@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757724204 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724204 Building ZINC000757724205 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757724205 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/404 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757724205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724205 none O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/405 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757724205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724205 none O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757724205 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 Building ZINC000757724205 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757724205 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 404) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757724205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724205 none O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 405) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000757724205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757724205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000757724205 none O=C(N[C@@H]1CC2(CCC2)Oc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757724205 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757724205 Building ZINC000757842000 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757842000 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/406 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000757842000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757842000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000757842000 none O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 15, 39, 39, 39, 39, 39, 1, 1, 1, 8, 8, 8, 8, 8, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/407 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000757842000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757842000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000757842000 none O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 13, 13, 13, 13, 17, 38, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 8, 13, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757842000 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 Building ZINC000757842000 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000757842000 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 406) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000757842000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000757842000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000757842000 none O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 15, 39, 39, 39, 39, 39, 1, 1, 1, 8, 8, 8, 8, 8, 6, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 407) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000757842000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000757842000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000757842000 none O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 13, 13, 13, 13, 17, 38, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 8, 8, 13, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000757842000 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000757842000 Building ZINC000759085856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759085856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/408 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759085856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085856 none Cc1nc2c(s1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 7, 10, 10, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/409 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759085856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085856 none Cc1nc2c(s1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 7, 11, 11, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000759085856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 Building ZINC000759085856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759085856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 408) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc2c(s1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759085856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085856 none Cc1nc2c(s1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 7, 10, 10, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 409) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc2c(s1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759085856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085856 none Cc1nc2c(s1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 7, 11, 11, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000759085856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085856 Building ZINC000759085858 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759085858 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/410 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759085858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085858 none Cc1nc2c(s1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 7, 12, 12, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/411 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759085858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085858 none Cc1nc2c(s1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 7, 10, 10, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000759085858 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 Building ZINC000759085858 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759085858 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 410) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc2c(s1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759085858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085858 none Cc1nc2c(s1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 7, 12, 12, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 411) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc2c(s1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2) `ZINC000759085858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759085858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000759085858 none Cc1nc2c(s1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 7, 10, 10, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000759085858 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000759085858 Building ZINC000907259730 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259730 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/412 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/413 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/414 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/414' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/415 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/415' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259730 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 Building ZINC000907259730 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259730 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 412) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 413) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 414) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 415) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259730 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 Building ZINC000907259730 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259730 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 412) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 413) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 414) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 415) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259730 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 Building ZINC000907259730 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259730 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 412) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 413) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 414) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 415) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1) `ZINC000907259730.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259730 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259730 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259730 Building ZINC000907259732 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259732 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/416 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/417 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/418 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/418' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/419 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/419' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259732 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 Building ZINC000907259732 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259732 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 416) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 417) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 418) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 419) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259732 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 Building ZINC000907259732 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259732 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 416) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 417) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 418) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 419) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259732 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 Building ZINC000907259732 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907259732 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 416) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 417) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 418) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 419) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1) `ZINC000907259732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907259732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907259732 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cnc(N2CCCC[C@H]2C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907259732 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907259732 Building ZINC000907289663 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907289663 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/420 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1) `ZINC000907289663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907289663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000907289663 none CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 12, 20, 20, 20, 20, 20, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/421 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1) `ZINC000907289663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907289663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000907289663 none CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 12, 20, 20, 20, 20, 20, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907289663 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 Building ZINC000907289663 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907289663 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 420) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1) `ZINC000907289663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907289663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000907289663 none CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 12, 20, 20, 20, 20, 20, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 421) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1) `ZINC000907289663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907289663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000907289663 none CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 4, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 12, 20, 20, 20, 20, 20, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907289663 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907289663 Building ZINC000907363862 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363862 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/422 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363862 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 17, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 59 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/423 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363862 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363862 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 Building ZINC000907363862 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363862 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 422) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363862 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 17, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 59 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 423) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363862 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363862 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363862 Building ZINC000907363863 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363863 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/424 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363863 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/425 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363863 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 7, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 18, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 58 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363863 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 Building ZINC000907363863 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363863 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 424) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363863 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 425) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1) `ZINC000907363863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363863 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 7, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 18, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 58 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363863 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363863 Building ZINC000907363864 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363864 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/426 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363864 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 4, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 47 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/427 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363864 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363864 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 Building ZINC000907363864 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363864 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 426) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363864 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 4, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 47 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 427) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363864 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363864 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363864 Building ZINC000907363865 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363865 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/428 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363865 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/429 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363865 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 18, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 61 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363865 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 Building ZINC000907363865 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907363865 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 428) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907363865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363865 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 429) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1) `ZINC000907363865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907363865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907363865 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCO[C@@H](c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 17, 17, 17, 17, 17, 17, 17, 18, 18, 17, 18, 18, 18, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 18, 18, 18, 18, 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]) total number of confs: 61 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907363865 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907363865 Building ZINC000907468407 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907468407 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/430 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12) `ZINC000907468407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907468407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000907468407 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 20, 20, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 5, 5, 5] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/431 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12) `ZINC000907468407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907468407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000907468407 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 20, 20, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 5, 5, 5] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907468407 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 Building ZINC000907468407 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907468407 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 430) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12) `ZINC000907468407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907468407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000907468407 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 20, 20, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 5, 5, 5] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 431) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12) `ZINC000907468407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907468407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000907468407 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)c2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 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, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 20, 20, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 20, 5, 5, 5] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907468407 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907468407 Building ZINC000907517655 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907517655 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/432 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1) `ZINC000907517655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907517655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907517655 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 16, 20, 20, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 10, 10, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/433 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1) `ZINC000907517655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907517655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907517655 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 16, 20, 20, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 10, 10, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907517655 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 Building ZINC000907517655 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907517655 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 432) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1) `ZINC000907517655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907517655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907517655 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 16, 20, 20, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 10, 10, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 433) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1) `ZINC000907517655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907517655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907517655 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)OC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 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, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 10, 16, 20, 20, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 10, 10, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907517655 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907517655 Building ZINC000907519896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907519896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/434 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/435 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/436 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/436' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/437 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/437' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907519896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 Building ZINC000907519896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907519896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 434) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 435) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 436) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 437) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907519896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 Building ZINC000907519896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907519896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 434) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 435) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 436) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 437) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907519896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 Building ZINC000907519896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000907519896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 434) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 435) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 436) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 10, 14, 14, 14, 22, 22, 22, 22, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 14, 14, 14, 22, 22, 14, 14] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 437) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2) `ZINC000907519896.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000907519896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000907519896 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c1CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 9, 13, 13, 13, 21, 21, 21, 21, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 13, 13, 13, 21, 21, 13, 13] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907519896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907519896 Building ZINC000907603539 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907603539 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/438 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1) `ZINC000907603539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907603539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907603539 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/439 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1) `ZINC000907603539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907603539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907603539 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 6, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907603539 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 Building ZINC000907603539 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907603539 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 438) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1) `ZINC000907603539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907603539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907603539 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 439) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1) `ZINC000907603539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907603539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000907603539 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3cccc(C)c3o2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 6, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907603539 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907603539 Building ZINC000907653460 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907653460 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/440 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC) `ZINC000907653460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907653460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653460 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 13, 18, 18, 18, 21, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 21, 21, 22, 22, 22] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/441 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC) `ZINC000907653460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907653460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653460 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 13, 13, 13, 18, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 13, 13, 13, 18, 18, 19, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907653460 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 Building ZINC000907653460 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907653460 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 440) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC) `ZINC000907653460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907653460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653460 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 13, 18, 18, 18, 21, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 21, 21, 22, 22, 22] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 441) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC) `ZINC000907653460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907653460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653460 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 10, 13, 13, 13, 18, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 13, 13, 13, 18, 18, 19, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907653460 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653460 Building ZINC000907653461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907653461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/442 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC) `ZINC000907653461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907653461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653461 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 9, 13, 13, 13, 19, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 13, 13, 13, 19, 19, 20, 20, 20] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/443 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC) `ZINC000907653461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907653461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653461 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 4, 4, 13, 18, 18, 18, 20, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 20, 20, 21, 21, 21] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907653461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 Building ZINC000907653461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907653461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 442) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC) `ZINC000907653461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907653461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653461 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 9, 13, 13, 13, 19, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 13, 13, 13, 19, 19, 20, 20, 20] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 443) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC) `ZINC000907653461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907653461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000907653461 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1O[C@@H](C)COC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 2, 4, 4, 4, 13, 18, 18, 18, 20, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 18, 18, 18, 20, 20, 21, 21, 21] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907653461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907653461 Building ZINC000907706573 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907706573 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/444 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br) `ZINC000907706573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907706573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907706573 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 6, 14, 17, 17, 14, 16, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 14, 14, 17, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/445 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br) `ZINC000907706573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907706573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907706573 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 6, 15, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907706573 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 Building ZINC000907706573 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907706573 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 444) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br) `ZINC000907706573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907706573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907706573 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 6, 14, 17, 17, 14, 16, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 14, 14, 17, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 445) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br) `ZINC000907706573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907706573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907706573 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(F)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 6, 15, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907706573 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907706573 Building ZINC000907726494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907726494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/446 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1) `ZINC000907726494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907726494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907726494 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 8, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/447 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1) `ZINC000907726494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907726494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907726494 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907726494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 Building ZINC000907726494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907726494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 446) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1) `ZINC000907726494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907726494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907726494 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 8, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 447) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1) `ZINC000907726494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907726494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000907726494 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 17, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 7, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907726494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907726494 Building ZINC000907773510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907773510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/448 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1) `ZINC000907773510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907773510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907773510 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/449 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1) `ZINC000907773510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907773510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907773510 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907773510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 Building ZINC000907773510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907773510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 448) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1) `ZINC000907773510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907773510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907773510 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 449) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1) `ZINC000907773510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907773510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907773510 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc(c2ncc3n2CCCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907773510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907773510 Building ZINC000907806158 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907806158 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/450 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1) `ZINC000907806158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907806158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907806158 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 10, 13, 18, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/451 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1) `ZINC000907806158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907806158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907806158 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 8, 12, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907806158 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 Building ZINC000907806158 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907806158 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 450) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1) `ZINC000907806158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907806158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907806158 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 10, 13, 18, 18, 18, 18, 18, 18, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 451) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1) `ZINC000907806158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907806158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000907806158 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C)c(C(=O)N2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 8, 12, 17, 17, 17, 17, 17, 17, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7] 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907806158 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907806158 Building ZINC000907809012 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907809012 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/452 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1) `ZINC000907809012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907809012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000907809012 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 10, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/453 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1) `ZINC000907809012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907809012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000907809012 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 10, 18, 18, 10, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907809012 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 Building ZINC000907809012 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907809012 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 452) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1) `ZINC000907809012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907809012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000907809012 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 10, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 17, 17, 17, 17, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 453) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1) `ZINC000907809012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907809012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000907809012 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccccc2F)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 10, 18, 18, 10, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 18, 18, 18, 18, 4] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907809012 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907809012 Building ZINC000907821461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907821461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/454 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C) `ZINC000907821461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907821461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000907821461 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 26, 26, 9, 9, 9] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/455 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C) `ZINC000907821461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907821461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000907821461 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 20, 20, 20, 20, 20, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 20, 20, 9, 9, 9] 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907821461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 Building ZINC000907821461 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907821461 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 454) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C) `ZINC000907821461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907821461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000907821461 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 26, 26, 9, 9, 9] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 455) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C) `ZINC000907821461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907821461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000907821461 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Cl)s2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 20, 20, 20, 20, 20, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 20, 20, 9, 9, 9] 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907821461 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907821461 Building ZINC000907866945 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907866945 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/456 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1) `ZINC000907866945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907866945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000907866945 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/457 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1) `ZINC000907866945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907866945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000907866945 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907866945 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 Building ZINC000907866945 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907866945 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 456) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1) `ZINC000907866945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907866945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000907866945 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 457) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1) `ZINC000907866945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907866945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000907866945 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nnc(c2cc(F)ccc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907866945 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907866945 Building ZINC000907894880 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907894880 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/458 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1) `ZINC000907894880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907894880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000907894880 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 9, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/459 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1) `ZINC000907894880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907894880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000907894880 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 8, 14, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907894880 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 Building ZINC000907894880 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907894880 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 458) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1) `ZINC000907894880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907894880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000907894880 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 9, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 459) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1) `ZINC000907894880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907894880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000907894880 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(n2c(C)nc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 8, 14, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907894880 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907894880 Building ZINC000123288894 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123288894 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/460 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(c3ccccc3)cc2)cn1) `ZINC000123288894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123288894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000123288894 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 8, 8, 6, 7, 14, 14, 6, 14, 14, 8, 8, 7, 7, 15, 15, 15, 15, 15, 7, 4, 6, 6, 6, 8, 8, 14, 14, 12, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/461 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(c3ccccc3)cc2)cn1) `ZINC000123288894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123288894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000123288894 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 6, 7, 14, 14, 14, 14, 14, 11, 11, 7, 7, 16, 16, 16, 16, 16, 7, 4, 6, 6, 6, 11, 11, 14, 14, 14, 14, 14, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000123288894 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 Building ZINC000123288894 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123288894 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 460) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(c3ccccc3)cc2)cn1) `ZINC000123288894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123288894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000123288894 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 8, 8, 6, 7, 14, 14, 6, 14, 14, 8, 8, 7, 7, 15, 15, 15, 15, 15, 7, 4, 6, 6, 6, 8, 8, 14, 14, 12, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 461) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(c3ccccc3)cc2)cn1) `ZINC000123288894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123288894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000123288894 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 11, 11, 6, 7, 14, 14, 14, 14, 14, 11, 11, 7, 7, 16, 16, 16, 16, 16, 7, 4, 6, 6, 6, 11, 11, 14, 14, 14, 14, 14, 11, 11, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000123288894 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123288894 Building ZINC000907936297 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907936297 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/462 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2) `ZINC000907936297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907936297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907936297 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/463 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2) `ZINC000907936297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907936297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907936297 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907936297 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 Building ZINC000907936297 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000907936297 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 462) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2) `ZINC000907936297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000907936297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907936297 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 463) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2) `ZINC000907936297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000907936297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000907936297 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1ncc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000907936297 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000907936297 Building ZINC000908017414 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908017414 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/464 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1) `ZINC000908017414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908017414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000908017414 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/465 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1) `ZINC000908017414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908017414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000908017414 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908017414 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 Building ZINC000908017414 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908017414 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 464) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1) `ZINC000908017414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908017414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000908017414 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 465) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1) `ZINC000908017414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908017414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000908017414 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)(F)F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 12, 17, 17, 17, 17, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 17, 17, 5] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908017414 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908017414 Building ZINC000908053215 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908053215 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/466 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1) `ZINC000908053215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908053215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908053215 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 7, 7, 7, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 7, 20, 20, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/467 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1) `ZINC000908053215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908053215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908053215 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 6, 6, 7, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 6, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908053215 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 Building ZINC000908053215 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908053215 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 466) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1) `ZINC000908053215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908053215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908053215 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 7, 7, 7, 20, 20, 20, 20, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 7, 20, 20, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 467) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1) `ZINC000908053215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908053215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908053215 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 6, 6, 7, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 6, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908053215 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908053215 Building ZINC000908055460 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908055460 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/468 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1) `ZINC000908055460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908055460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000908055460 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/469 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1) `ZINC000908055460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908055460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000908055460 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908055460 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 Building ZINC000908055460 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908055460 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 468) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1) `ZINC000908055460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908055460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000908055460 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 469) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1) `ZINC000908055460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908055460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000908055460 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Cc2nc(C(C)C)no2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908055460 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908055460 Building ZINC000908124233 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908124233 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/470 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21) `ZINC000908124233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908124233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000908124233 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 18, 18] 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]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/471 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21) `ZINC000908124233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908124233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000908124233 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 17, 17, 17, 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]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908124233 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 Building ZINC000908124233 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908124233 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 470) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21) `ZINC000908124233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908124233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000908124233 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 18, 18] 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]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 471) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21) `ZINC000908124233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908124233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000908124233 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2cc(Br)cnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 17, 17, 17, 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]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908124233 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908124233 Building ZINC000908127074 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908127074 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/472 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1) `ZINC000908127074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908127074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908127074 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 6, 18, 18, 6, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/473 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1) `ZINC000908127074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908127074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908127074 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 6, 18, 18, 6, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908127074 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 Building ZINC000908127074 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908127074 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 472) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1) `ZINC000908127074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908127074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908127074 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 6, 18, 18, 6, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 473) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1) `ZINC000908127074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908127074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908127074 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(OCC(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 6, 18, 18, 6, 6] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908127074 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908127074 Building ZINC000760513027 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760513027 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/474 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1) `ZINC000760513027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760513027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000760513027 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 6, 6, 6, 8, 15, 15, 8, 11, 15, 15, 10, 10, 10, 10, 10, 6, 6, 13, 13, 13, 6, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/475 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1) `ZINC000760513027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760513027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000760513027 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 5, 1, 5, 1, 1, 1, 8, 8, 2, 8, 13, 8, 8, 8, 9, 15, 15, 13, 15, 15, 15, 11, 11, 11, 11, 11, 8, 8, 13, 13, 13, 8, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000760513027 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 Building ZINC000760513027 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760513027 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 474) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1) `ZINC000760513027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760513027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000760513027 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 6, 6, 6, 8, 15, 15, 8, 11, 15, 15, 10, 10, 10, 10, 10, 6, 6, 13, 13, 13, 6, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 475) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1) `ZINC000760513027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760513027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000760513027 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 5, 1, 5, 1, 1, 1, 8, 8, 2, 8, 13, 8, 8, 8, 9, 15, 15, 13, 15, 15, 15, 11, 11, 11, 11, 11, 8, 8, 13, 13, 13, 8, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000760513027 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000760513027 Building ZINC000908232856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908232856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/476 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F) `ZINC000908232856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908232856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232856 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/477 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F) `ZINC000908232856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908232856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232856 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 21, 21, 21] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908232856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 Building ZINC000908232856 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908232856 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 476) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F) `ZINC000908232856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908232856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232856 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 20, 20, 20] 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]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 477) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F) `ZINC000908232856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908232856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232856 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 21, 21, 21] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908232856 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232856 Building ZINC000908232858 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908232858 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/478 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F) `ZINC000908232858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908232858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232858 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 21, 21, 21] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/479 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F) `ZINC000908232858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908232858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232858 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 20, 20, 20] 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]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908232858 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 Building ZINC000908232858 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908232858 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 478) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F) `ZINC000908232858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908232858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232858 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 4, 6, 6, 6, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 21, 21, 21] 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 479) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F) `ZINC000908232858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908232858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000908232858 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1O[C@H](C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 5, 5, 20, 20, 20] 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]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908232858 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908232858 Building ZINC000908261272 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908261272 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/480 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1) `ZINC000908261272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908261272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000908261272 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 7, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 8, 8] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/481 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1) `ZINC000908261272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908261272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000908261272 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 8, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908261272 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 Building ZINC000908261272 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908261272 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 480) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1) `ZINC000908261272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908261272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000908261272 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 7, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 8, 8] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 481) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1) `ZINC000908261272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908261272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000908261272 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2noc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 15, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 8, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 9, 9] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908261272 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908261272 Building ZINC000908270005 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908270005 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/482 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1) `ZINC000908270005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908270005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270005 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 9, 12, 13, 13, 12, 13, 15, 13, 13, 9, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 13, 13, 15, 15, 15, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 48 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]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/483 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1) `ZINC000908270005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908270005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270005 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 11, 15, 15, 11, 15, 16, 15, 15, 7, 10, 10, 10, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 15, 15, 16, 16, 16, 15, 15, 10, 10, 10, 11, 11, 11, 11, 11] 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]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908270005 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 Building ZINC000908270005 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908270005 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 482) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1) `ZINC000908270005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908270005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270005 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 3, 3, 9, 12, 13, 13, 12, 13, 15, 13, 13, 9, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 13, 13, 15, 15, 15, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 48 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]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 483) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1) `ZINC000908270005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908270005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270005 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 11, 15, 15, 11, 15, 16, 15, 15, 7, 10, 10, 10, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 15, 15, 16, 16, 16, 15, 15, 10, 10, 10, 11, 11, 11, 11, 11] 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]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908270005 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270005 Building ZINC000908270006 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908270006 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/484 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1) `ZINC000908270006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908270006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270006 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 12, 14, 14, 12, 14, 18, 14, 14, 7, 11, 11, 11, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 14, 14, 18, 18, 18, 14, 14, 11, 11, 11, 13, 13, 13, 13, 13] 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]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/485 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1) `ZINC000908270006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908270006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270006 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 10, 14, 14, 10, 14, 15, 14, 14, 7, 12, 12, 12, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 15, 15, 15, 14, 14, 12, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 106 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908270006 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 Building ZINC000908270006 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908270006 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 484) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1) `ZINC000908270006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908270006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270006 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 12, 14, 14, 12, 14, 18, 14, 14, 7, 11, 11, 11, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 14, 14, 18, 18, 18, 14, 14, 11, 11, 11, 13, 13, 13, 13, 13] 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]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 485) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1) `ZINC000908270006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908270006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000908270006 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(OC)cc1)[C@H](C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 7, 10, 14, 14, 10, 14, 15, 14, 14, 7, 12, 12, 12, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 14, 14, 15, 15, 15, 14, 14, 12, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 106 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908270006 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908270006 Building ZINC000844779313 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844779313 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/486 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C) `ZINC000844779313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844779313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844779313 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/487 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C) `ZINC000844779313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844779313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844779313 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 25, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844779313 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 Building ZINC000844779313 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844779313 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 486) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C) `ZINC000844779313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844779313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844779313 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 487) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C) `ZINC000844779313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844779313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844779313 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])C2CCSCC2)oc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 5, 7, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 25, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844779313 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779313 Building ZINC000844779790 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844779790 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/488 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000844779790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844779790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000844779790 none CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 10, 7, 5, 7, 25, 41, 41, 41, 41, 41, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 15, 15, 16, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/489 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000844779790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844779790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000844779790 none CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 22, 10, 6, 5, 6, 26, 45, 45, 45, 45, 45, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 18, 18, 16, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844779790 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 Building ZINC000844779790 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844779790 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 488) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000844779790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844779790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000844779790 none CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 18, 10, 7, 5, 7, 25, 41, 41, 41, 41, 41, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 15, 15, 16, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 489) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000844779790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844779790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000844779790 none CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 22, 10, 6, 5, 6, 26, 45, 45, 45, 45, 45, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 18, 18, 16, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844779790 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844779790 Building ZINC000595966921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000595966921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/490 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000595966921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000595966921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000595966921 none Cc1cc(F)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/491 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000595966921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000595966921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000595966921 none Cc1cc(F)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000595966921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 Building ZINC000595966921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000595966921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 490) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(F)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000595966921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000595966921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000595966921 none Cc1cc(F)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 491) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(F)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000595966921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000595966921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000595966921 none Cc1cc(F)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000595966921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000595966921 Building ZINC000908576869 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908576869 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/492 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1) `ZINC000908576869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908576869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000908576869 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12] 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]) total number of confs: 41 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/493 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1) `ZINC000908576869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908576869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000908576869 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 8, 11, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908576869 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 Building ZINC000908576869 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908576869 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 492) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1) `ZINC000908576869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908576869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000908576869 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12] 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]) total number of confs: 41 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 493) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1) `ZINC000908576869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908576869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000908576869 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2ccnc3ccccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 8, 11, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908576869 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908576869 Building ZINC000844960000 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844960000 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/494 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000844960000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844960000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960000 none COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 16, 16, 16, 16, 16, 5, 16, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/495 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000844960000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844960000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960000 none COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 13, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844960000 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 Building ZINC000844960000 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844960000 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 494) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000844960000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844960000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960000 none COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 16, 16, 16, 16, 16, 5, 16, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 495) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000844960000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844960000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960000 none COc1ccc(Cl)c2c1CCC[C@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 13, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844960000 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960000 Building ZINC000844960001 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844960001 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/496 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000844960001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844960001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960001 none COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 13, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 35 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/497 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000844960001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844960001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960001 none COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 16, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844960001 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 Building ZINC000844960001 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000844960001 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 496) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000844960001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000844960001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960001 none COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 13, 3, 5, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 35 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 497) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000844960001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000844960001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000844960001 none COc1ccc(Cl)c2c1CCC[C@@H]2N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 16, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000844960001 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000844960001 Building ZINC000845018917 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000845018917 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/498 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C(F)F) `ZINC000845018917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000845018917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000845018917 none Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 43, 43, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 48, 48, 43, 43, 43, 43, 35, 43, 43, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/499 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C(F)F) `ZINC000845018917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000845018917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000845018917 none Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 40, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 18, 18, 45, 45, 40, 40, 40, 40, 18, 40, 40, 18, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45] 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]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000845018917 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 Building ZINC000845018917 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000845018917 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 498) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C(F)F) `ZINC000845018917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000845018917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000845018917 none Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 43, 43, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 17, 17, 48, 48, 43, 43, 43, 43, 35, 43, 43, 17, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 499) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C(F)F) `ZINC000845018917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000845018917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000845018917 none Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 40, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 18, 18, 45, 45, 40, 40, 40, 40, 18, 40, 40, 18, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45] 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]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000845018917 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000845018917 Building ZINC000908852232 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908852232 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/500 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908852232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852232 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 12, 12, 12, 17, 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]) total number of confs: 60 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/501 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908852232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852232 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 4, 4, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 17, 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]) total number of confs: 61 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908852232 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 Building ZINC000908852232 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908852232 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 500) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908852232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852232 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 12, 12, 12, 17, 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]) total number of confs: 60 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 501) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908852232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852232 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 4, 4, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 17, 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]) total number of confs: 61 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908852232 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852232 Building ZINC000908852233 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908852233 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/502 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908852233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852233 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 4, 4, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 17, 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]) total number of confs: 61 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/503 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908852233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852233 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 13, 17, 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]) total number of confs: 64 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908852233 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 Building ZINC000908852233 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000908852233 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 502) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000908852233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852233 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 4, 4, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 17, 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]) total number of confs: 61 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 503) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC000908852233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000908852233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000908852233 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 13, 17, 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]) total number of confs: 64 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000908852233 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000908852233 Building ZINC000909272585 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909272585 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/504 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1) `ZINC000909272585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909272585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272585 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 10, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/505 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1) `ZINC000909272585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909272585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272585 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18] 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]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909272585 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 Building ZINC000909272585 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909272585 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 504) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1) `ZINC000909272585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909272585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272585 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 10, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 505) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1) `ZINC000909272585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909272585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272585 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18] 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]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909272585 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272585 Building ZINC000909272587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909272587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/506 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1) `ZINC000909272587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909272587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272587 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 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]) total number of confs: 41 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/507 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1) `ZINC000909272587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909272587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272587 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909272587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 Building ZINC000909272587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909272587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 506) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1) `ZINC000909272587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909272587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272587 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 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]) total number of confs: 41 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 507) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1) `ZINC000909272587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909272587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000909272587 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909272587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909272587 Building ZINC000909260758 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909260758 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/508 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12) `ZINC000909260758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909260758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000909260758 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17, 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]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/509 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12) `ZINC000909260758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909260758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000909260758 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17, 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]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909260758 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 Building ZINC000909260758 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909260758 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 508) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12) `ZINC000909260758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909260758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000909260758 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17, 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]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 509) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12) `ZINC000909260758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909260758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000909260758 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1cccc2c(Br)ccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [11, 10, 1, 10, 10, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 6, 17, 17, 17, 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]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909260758 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909260758 Building ZINC000909328511 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909328511 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/510 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC000909328511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909328511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000909328511 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 19, 19, 19, 19, 5, 5] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/511 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC000909328511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909328511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000909328511 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909328511 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 Building ZINC000909328511 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909328511 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 510) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC000909328511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909328511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000909328511 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 19, 19, 19, 19, 5, 5] 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 511) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC000909328511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909328511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000909328511 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909328511 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909328511 Building ZINC000909572287 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000909572287 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/512 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/513 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/514 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/514' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/515 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/515' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909572287 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 Building ZINC000909572287 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000909572287 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 512) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 513) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 514) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 515) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909572287 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 Building ZINC000909572287 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000909572287 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 512) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 513) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 514) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 515) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909572287 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 Building ZINC000909572287 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000909572287 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 512) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 513) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 514) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 11, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 515) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2) `ZINC000909572287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000909572287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909572287 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(CC(F)(F)F)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 9, 11, 11, 6, 11, 11, 11, 18, 18, 18, 18, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 11, 10, 11, 11, 18, 18, 11, 11] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909572287 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909572287 Building ZINC000909890703 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909890703 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/516 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1) `ZINC000909890703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909890703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909890703 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 8, 20, 21, 21, 20, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 20, 20, 21, 21, 21, 21, 21] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/517 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1) `ZINC000909890703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909890703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909890703 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 8, 20, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 20, 20, 21, 21, 21, 21, 21] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909890703 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 Building ZINC000909890703 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000909890703 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 516) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1) `ZINC000909890703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000909890703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909890703 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 8, 20, 21, 21, 20, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 20, 20, 21, 21, 21, 21, 21] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 517) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1) `ZINC000909890703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000909890703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000909890703 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 8, 20, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 20, 20, 21, 21, 21, 21, 21] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000909890703 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000909890703 Building ZINC000846426627 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000846426627 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/518 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2)c1) `ZINC000846426627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000846426627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000846426627 none COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/519 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2)c1) `ZINC000846426627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000846426627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000846426627 none COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000846426627 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 Building ZINC000846426627 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000846426627 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 518) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2)c1) `ZINC000846426627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000846426627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000846426627 none COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 519) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2)c1) `ZINC000846426627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000846426627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000846426627 none COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000846426627 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846426627 Building ZINC000108984069 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108984069 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/520 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1) `ZINC000108984069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108984069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000108984069 none Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/521 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1) `ZINC000108984069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108984069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000108984069 none Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 22, 22, 22, 22, 22, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108984069 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 Building ZINC000108984069 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108984069 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 520) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1) `ZINC000108984069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108984069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000108984069 none Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 521) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1) `ZINC000108984069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108984069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000108984069 none Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 22, 22, 22, 22, 22, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108984069 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108984069 Building ZINC000109111635 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000109111635 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/522 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccsc2)ns1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000109111635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109111635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000109111635 none O=C(Nc1nc(c2ccsc2)ns1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 14, 1, 8, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 46, 46, 46, 46, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 46, 46, 46, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/523 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccsc2)ns1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000109111635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109111635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000109111635 none O=C(Nc1nc(c2ccsc2)ns1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 14, 1, 8, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 46, 46, 46, 46, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 46, 46, 46, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000109111635 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 Building ZINC000109111635 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000109111635 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 522) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(c2ccsc2)ns1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000109111635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109111635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000109111635 none O=C(Nc1nc(c2ccsc2)ns1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 14, 1, 8, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 17, 17, 17, 46, 46, 46, 46, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 46, 46, 46, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 523) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(c2ccsc2)ns1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000109111635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109111635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000109111635 none O=C(Nc1nc(c2ccsc2)ns1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 14, 1, 8, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 46, 46, 46, 46, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 46, 46, 46, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000109111635 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000109111635 Building ZINC000114269016 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000114269016 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/524 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000114269016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269016 none CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 7, 18, 18, 4, 7, 12, 12, 12, 12, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8] 49 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]) total number of confs: 120 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/525 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000114269016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269016 none CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 26, 10, 19, 19, 5, 10, 16, 16, 16, 16, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000114269016 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 Building ZINC000114269016 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000114269016 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 524) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)[C@@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000114269016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269016 none CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 7, 18, 18, 4, 7, 12, 12, 12, 12, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8] 49 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]) total number of confs: 120 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 525) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)[C@@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000114269016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269016 none CC(C)[C@@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 26, 10, 19, 19, 5, 10, 16, 16, 16, 16, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000114269016 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269016 Building ZINC000114269020 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000114269020 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/526 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000114269020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269020 none CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 11, 20, 20, 5, 11, 17, 17, 17, 17, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/527 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000114269020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269020 none CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 7, 19, 19, 4, 7, 11, 11, 11, 11, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 19, 19, 19, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 49 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]) total number of confs: 115 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000114269020 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 Building ZINC000114269020 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000114269020 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 526) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000114269020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269020 none CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 11, 20, 20, 5, 11, 17, 17, 17, 17, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 20, 20, 20, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 527) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000114269020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000114269020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000114269020 none CC(C)[C@H](C)N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 7, 19, 19, 4, 7, 11, 11, 11, 11, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 19, 19, 19, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 49 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]) total number of confs: 115 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000114269020 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000114269020 Building ZINC000846555304 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000846555304 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/528 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000846555304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000846555304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000846555304 none CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 23, 11, 6, 3, 6, 24, 37, 37, 37, 37, 37, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 23, 23, 23, 23, 20, 20, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 2, 4, 2, 2] 100 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/529 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000846555304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000846555304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000846555304 none CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 20, 25, 13, 6, 3, 6, 22, 36, 36, 36, 36, 36, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 25, 25, 25, 25, 25, 25, 20, 20, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 4, 2, 2] 100 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000846555304 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 Building ZINC000846555304 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000846555304 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 528) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000846555304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000846555304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000846555304 none CC(C)CON(CC1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 23, 11, 6, 3, 6, 24, 37, 37, 37, 37, 37, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 23, 23, 23, 23, 20, 20, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 2, 4, 2, 2] 100 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 529) grep: /scratch/xiaobo/132203/xbs-8058115.45/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)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000846555304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000846555304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000846555304 none CC(C)CON(CC1CCCCC1)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 20, 25, 13, 6, 3, 6, 22, 36, 36, 36, 36, 36, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 25, 25, 25, 25, 25, 25, 25, 20, 20, 15, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 4, 2, 2] 100 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000846555304 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000846555304 Building ZINC000185540220 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185540220 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/530 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)cc1) `ZINC000185540220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185540220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540220 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 11, 11, 34, 34, 34, 43, 43, 34, 35, 43, 43, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 34, 34, 34, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/531 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)cc1) `ZINC000185540220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185540220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540220 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 10, 10, 33, 33, 33, 41, 41, 33, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 33, 33, 33, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185540220 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 Building ZINC000185540220 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185540220 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 530) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)cc1) `ZINC000185540220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185540220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540220 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 11, 11, 34, 34, 34, 43, 43, 34, 35, 43, 43, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 34, 34, 34, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 531) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)cc1) `ZINC000185540220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185540220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540220 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 10, 10, 33, 33, 33, 41, 41, 33, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 33, 33, 33, 41, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185540220 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540220 Building ZINC000185540236 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185540236 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/532 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)cc1) `ZINC000185540236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185540236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540236 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 10, 10, 33, 33, 33, 42, 42, 33, 33, 42, 42, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 33, 33, 33, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/533 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)cc1) `ZINC000185540236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185540236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540236 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 12, 12, 37, 37, 37, 45, 45, 37, 43, 44, 45, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 37, 37, 37, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185540236 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 Building ZINC000185540236 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185540236 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 532) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)cc1) `ZINC000185540236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185540236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540236 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 10, 10, 33, 33, 33, 42, 42, 33, 33, 42, 42, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 33, 33, 33, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 533) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)cc1) `ZINC000185540236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185540236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185540236 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1ccc(Cl)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 12, 12, 37, 37, 37, 45, 45, 37, 43, 44, 45, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 37, 37, 37, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185540236 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185540236 Building ZINC000185597318 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185597318 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/534 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185597318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597318 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 50, 50, 50, 38, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 10, 10, 10, 6, 4, 4, 4, 4] 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]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/535 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185597318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597318 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185597318 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 Building ZINC000185597318 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185597318 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 534) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185597318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597318 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 50, 50, 50, 38, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 10, 10, 10, 6, 4, 4, 4, 4] 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]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 535) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185597318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597318 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185597318 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597318 Building ZINC000185597333 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185597333 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/536 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185597333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597333 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/537 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185597333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597333 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 36, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 10, 10, 10, 6, 5, 5, 5, 5] 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]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185597333 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 Building ZINC000185597333 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185597333 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 536) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185597333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597333 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 537) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185597333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185597333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000185597333 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 36, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 10, 10, 10, 6, 5, 5, 5, 5] 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]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185597333 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185597333 Building ZINC000185767308 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185767308 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/538 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2ccccc2C2(CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185767308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185767308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000185767308 none O=C(N1Cc2ccccc2C2(CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 1, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/539 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2ccccc2C2(CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185767308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185767308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000185767308 none O=C(N1Cc2ccccc2C2(CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 1, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4] 42 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185767308 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 Building ZINC000185767308 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185767308 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 538) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1Cc2ccccc2C2(CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185767308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185767308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000185767308 none O=C(N1Cc2ccccc2C2(CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 1, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 539) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1Cc2ccccc2C2(CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000185767308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185767308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000185767308 none O=C(N1Cc2ccccc2C2(CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 1, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4] 42 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000185767308 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000185767308 Building ZINC000186023246 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186023246 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/540 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl) `ZINC000186023246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186023246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023246 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 34, 34, 22, 23, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 8, 17, 17, 17, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/541 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl) `ZINC000186023246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186023246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023246 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 38, 38, 23, 26, 38, 38, 38, 8, 8, 8, 6, 6, 6, 6, 8, 18, 18, 18, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186023246 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 Building ZINC000186023246 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186023246 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 540) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl) `ZINC000186023246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186023246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023246 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 34, 34, 22, 23, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 8, 17, 17, 17, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 541) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl) `ZINC000186023246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186023246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023246 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 38, 38, 23, 26, 38, 38, 38, 8, 8, 8, 6, 6, 6, 6, 8, 18, 18, 18, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186023246 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023246 Building ZINC000186023267 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186023267 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/542 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl) `ZINC000186023267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186023267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023267 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 38, 38, 18, 26, 38, 38, 38, 8, 8, 8, 6, 6, 6, 6, 8, 18, 18, 18, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/543 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl) `ZINC000186023267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186023267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023267 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 34, 34, 17, 23, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 8, 17, 17, 17, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186023267 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 Building ZINC000186023267 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186023267 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 542) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl) `ZINC000186023267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186023267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023267 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 8, 18, 18, 18, 38, 38, 18, 26, 38, 38, 38, 8, 8, 8, 6, 6, 6, 6, 8, 18, 18, 18, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 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: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 543) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl) `ZINC000186023267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186023267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000186023267 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 34, 34, 17, 23, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 8, 17, 17, 17, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 156 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186023267 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186023267 Building ZINC000186048575 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186048575 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/544 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1) `ZINC000186048575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186048575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186048575 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 17, 34, 34, 34, 34, 8, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 17, 17, 34, 34, 34, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/545 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1) `ZINC000186048575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186048575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186048575 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 7, 14, 31, 31, 31, 31, 7, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186048575 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 Building ZINC000186048575 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186048575 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 544) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1) `ZINC000186048575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186048575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186048575 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 17, 34, 34, 34, 34, 8, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 17, 17, 34, 34, 34, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 545) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1) `ZINC000186048575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186048575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186048575 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccoc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 7, 14, 31, 31, 31, 31, 7, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186048575 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186048575 Building ZINC000186185684 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185684 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/546 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl) `ZINC000186185684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000186185684 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 12, 12, 21, 21, 21, 16, 21, 21, 21, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 21, 16, 21] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/547 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl) `ZINC000186185684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000186185684 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 12, 12, 20, 20, 20, 16, 20, 20, 20, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 20, 16, 20] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186185684 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 Building ZINC000186185684 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185684 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 546) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl) `ZINC000186185684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000186185684 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 12, 12, 21, 21, 21, 16, 21, 21, 21, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 21, 16, 21] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 547) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl) `ZINC000186185684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000186185684 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 12, 12, 20, 20, 20, 16, 20, 20, 20, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 20, 16, 20] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186185684 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186185684 Building ZINC000186214542 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186214542 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/548 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1) `ZINC000186214542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186214542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000186214542 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 10, 26, 37, 37, 33, 37, 37, 10, 26, 26, 14, 26, 26, 4, 4, 4, 4, 4, 4, 4, 26, 26, 37, 37, 37, 37, 37, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/549 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1) `ZINC000186214542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186214542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000186214542 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 11, 28, 38, 38, 30, 38, 38, 11, 27, 27, 15, 27, 27, 4, 4, 4, 4, 4, 4, 4, 28, 28, 38, 38, 38, 38, 38, 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186214542 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 Building ZINC000186214542 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186214542 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 548) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1) `ZINC000186214542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186214542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000186214542 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 10, 26, 37, 37, 33, 37, 37, 10, 26, 26, 14, 26, 26, 4, 4, 4, 4, 4, 4, 4, 26, 26, 37, 37, 37, 37, 37, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 549) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1) `ZINC000186214542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186214542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000186214542 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 11, 28, 38, 38, 30, 38, 38, 11, 27, 27, 15, 27, 27, 4, 4, 4, 4, 4, 4, 4, 28, 28, 38, 38, 38, 38, 38, 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]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186214542 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186214542 Building ZINC000186273656 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273656 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/550 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)C1) `ZINC000186273656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273656 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 17, 17, 17, 17, 17, 44, 44, 44, 17, 44, 44, 44, 17, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 44, 44, 44, 44, 17, 44, 44, 44, 44, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/551 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)C1) `ZINC000186273656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273656 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 43, 43, 43, 15, 43, 43, 43, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 43, 43, 43, 43, 15, 43, 43, 43, 43, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186273656 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 Building ZINC000186273656 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273656 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 550) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)C1) `ZINC000186273656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273656 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 17, 17, 17, 17, 17, 44, 44, 44, 17, 44, 44, 44, 17, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 44, 44, 44, 44, 17, 44, 44, 44, 44, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 551) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)C1) `ZINC000186273656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273656 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 43, 43, 43, 15, 43, 43, 43, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 43, 43, 43, 43, 15, 43, 43, 43, 43, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186273656 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273656 Building ZINC000186273676 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273676 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/552 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)C1) `ZINC000186273676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273676 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 7, 18, 18, 18, 18, 18, 45, 45, 45, 21, 45, 45, 45, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 45, 45, 45, 45, 30, 45, 45, 45, 45, 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]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/553 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)C1) `ZINC000186273676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273676 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 4, 15, 15, 15, 15, 15, 43, 43, 43, 15, 43, 43, 43, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 43, 43, 43, 43, 15, 43, 43, 43, 43, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186273676 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 Building ZINC000186273676 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273676 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 552) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)C1) `ZINC000186273676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273676 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 7, 18, 18, 18, 18, 18, 45, 45, 45, 21, 45, 45, 45, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 45, 45, 45, 45, 30, 45, 45, 45, 45, 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]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 553) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)C1) `ZINC000186273676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186273676 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cc(C)cc(C)c2)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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 4, 15, 15, 15, 15, 15, 43, 43, 43, 15, 43, 43, 43, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 43, 43, 43, 43, 15, 43, 43, 43, 43, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000186273676 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000186273676 Building ZINC000117721928 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117721928 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/554 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000117721928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117721928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000117721928 none O=C(N1CC=C(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 16, 16, 16, 16, 3, 3, 3, 3] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/555 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000117721928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117721928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000117721928 none O=C(N1CC=C(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000117721928 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 Building ZINC000117721928 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117721928 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 554) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC=C(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000117721928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117721928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000117721928 none O=C(N1CC=C(c2cccs2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 16, 16, 16, 16, 3, 3, 3, 3] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 555) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC=C(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000117721928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117721928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000117721928 none O=C(N1CC=C(c2cccs2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000117721928 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117721928 Building ZINC000187120801 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187120801 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/556 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187120801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120801 none Cc1nc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/557 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187120801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120801 none Cc1nc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000187120801 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 Building ZINC000187120801 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187120801 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 556) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187120801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120801 none Cc1nc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 557) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187120801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120801 none Cc1nc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 15, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000187120801 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120801 Building ZINC000171412036 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171412036 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/558 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1) `ZINC000171412036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171412036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000171412036 none Cc1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/559 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1) `ZINC000171412036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171412036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000171412036 none Cc1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000171412036 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 Building ZINC000171412036 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171412036 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 558) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1) `ZINC000171412036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171412036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000171412036 none Cc1csc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 1, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 559) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1) `ZINC000171412036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171412036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000171412036 none Cc1csc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000171412036 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000171412036 Building ZINC000679526171 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526171 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/560 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526171 none C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 15, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/561 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526171 none C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526171 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 Building ZINC000679526171 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526171 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 560) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526171 none C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 15, 2, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 561) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526171 none C[C@@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526171 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526171 Building ZINC000679526174 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526174 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/562 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526174 none C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 18, 2, 18, 1, 1, 1, 9, 9, 13, 13, 9, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 13, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/563 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526174 none C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526174 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 Building ZINC000679526174 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526174 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 562) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526174 none C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 18, 2, 18, 1, 1, 1, 9, 9, 13, 13, 9, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 13, 13, 13, 13, 13, 13, 13, 13] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 563) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526174 none C[C@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526174 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526174 Building ZINC000187120785 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187120785 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/564 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187120785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120785 none Cc1nc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/565 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187120785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120785 none Cc1nc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000187120785 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 Building ZINC000187120785 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187120785 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 564) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187120785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120785 none Cc1nc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 565) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1) `ZINC000187120785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187120785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000187120785 none Cc1nc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000187120785 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000187120785 Building ZINC000191302569 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191302569 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/566 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC000191302569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191302569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302569 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 19, 2, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40, 40, 40] 43 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/567 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC000191302569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191302569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302569 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 20, 2, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40, 40, 40] 44 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000191302569 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 Building ZINC000191302569 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191302569 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 566) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC000191302569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191302569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302569 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 19, 2, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40, 40, 40] 43 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 567) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC000191302569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191302569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302569 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 20, 2, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40, 40, 40] 44 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000191302569 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302569 Building ZINC000191302584 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191302584 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/568 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC000191302584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191302584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302584 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 23, 2, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 41, 41, 41, 41] 42 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/569 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC000191302584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191302584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302584 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 23, 2, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 39, 39, 39, 39] 41 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000191302584 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 Building ZINC000191302584 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191302584 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 568) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC000191302584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191302584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302584 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 23, 2, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 41, 41, 41, 41] 42 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 569) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC000191302584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191302584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000191302584 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 23, 2, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 39, 39, 39, 39] 41 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000191302584 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000191302584 Building ZINC000194203812 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194203812 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/570 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194203812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194203812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194203812 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 20, 20, 20, 20, 20, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/571 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194203812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194203812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194203812 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 18, 18, 18, 18, 18, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194203812 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 Building ZINC000194203812 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194203812 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 570) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194203812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194203812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194203812 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 20, 20, 20, 20, 20, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 571) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194203812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194203812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194203812 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 18, 18, 18, 18, 18, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194203812 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194203812 Building ZINC000194207896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194207896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/572 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194207896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194207896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000194207896 none CN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 26, 22, 24, 26, 26, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/573 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194207896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194207896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000194207896 none CN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 26, 22, 22, 26, 26, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194207896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 Building ZINC000194207896 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194207896 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 572) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194207896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194207896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000194207896 none CN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 26, 22, 24, 26, 26, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 573) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194207896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194207896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000194207896 none CN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 26, 26, 22, 22, 26, 26, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194207896 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194207896 Building ZINC000194238838 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194238838 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/574 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccco1)C1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194238838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194238838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000194238838 none O=C(N(Cc1ccco1)C1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 13, 20, 20, 20, 20, 5, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/575 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccco1)C1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194238838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194238838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000194238838 none O=C(N(Cc1ccco1)C1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 23, 23, 23, 23, 7, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194238838 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 Building ZINC000194238838 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194238838 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 574) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(Cc1ccco1)C1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194238838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194238838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000194238838 none O=C(N(Cc1ccco1)C1CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 13, 20, 20, 20, 20, 5, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 575) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(Cc1ccco1)C1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000194238838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194238838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000194238838 none O=C(N(Cc1ccco1)C1CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 5, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 16, 23, 23, 23, 23, 7, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194238838 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194238838 Building ZINC000194377854 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194377854 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/576 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194377854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377854 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 10, 23, 23, 10, 10, 46, 50, 50, 50, 46, 23, 23, 10, 10, 10, 5, 3, 3, 1, 3, 3, 23, 23, 49, 50, 50, 47, 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]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/577 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194377854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377854 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 25, 25, 9, 9, 45, 50, 50, 50, 45, 25, 25, 9, 9, 9, 5, 3, 3, 1, 3, 3, 25, 25, 45, 50, 50, 45, 25, 25] 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]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194377854 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 Building ZINC000194377854 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194377854 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 576) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194377854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377854 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 10, 23, 23, 10, 10, 46, 50, 50, 50, 46, 23, 23, 10, 10, 10, 5, 3, 3, 1, 3, 3, 23, 23, 49, 50, 50, 47, 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]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 577) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194377854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377854 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 25, 25, 9, 9, 45, 50, 50, 50, 45, 25, 25, 9, 9, 9, 5, 3, 3, 1, 3, 3, 25, 25, 45, 50, 50, 45, 25, 25] 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]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194377854 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377854 Building ZINC000194377867 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194377867 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/578 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194377867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377867 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 25, 25, 9, 9, 46, 46, 46, 46, 46, 25, 25, 9, 9, 9, 5, 3, 3, 1, 3, 3, 25, 25, 46, 47, 50, 46, 25, 25] 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]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/579 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194377867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377867 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 10, 24, 24, 15, 10, 44, 44, 45, 44, 44, 24, 24, 10, 10, 10, 5, 3, 3, 1, 3, 3, 24, 24, 44, 45, 45, 44, 24, 24] 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]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194377867 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 Building ZINC000194377867 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194377867 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 578) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194377867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377867 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 9, 25, 25, 9, 9, 46, 46, 46, 46, 46, 25, 25, 9, 9, 9, 5, 3, 3, 1, 3, 3, 25, 25, 46, 47, 50, 46, 25, 25] 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]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 579) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1) `ZINC000194377867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194377867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000194377867 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccc(c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 10, 24, 24, 15, 10, 44, 44, 45, 44, 44, 24, 24, 10, 10, 10, 5, 3, 3, 1, 3, 3, 24, 24, 44, 45, 45, 44, 24, 24] 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]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194377867 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194377867 Building ZINC000194544479 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194544479 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/580 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194544479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194544479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544479 none O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/581 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194544479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194544479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544479 none O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194544479 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 Building ZINC000194544479 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194544479 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 580) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194544479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194544479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544479 none O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 581) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194544479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194544479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544479 none O=C(N[C@@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194544479 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544479 Building ZINC000194544493 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194544493 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/582 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194544493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194544493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544493 none O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/583 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194544493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194544493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544493 none O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194544493 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 Building ZINC000194544493 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194544493 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 582) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194544493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194544493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544493 none O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 583) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194544493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194544493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000194544493 none O=C(N[C@H]1CCCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 5, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 1, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194544493 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194544493 Building ZINC000194557019 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194557019 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/584 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194557019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194557019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557019 none O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 1, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/585 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194557019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194557019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557019 none O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 1, 1, 1, 5, 5, 1, 5, 5, 7, 48, 48, 48, 5, 5, 2, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194557019 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 Building ZINC000194557019 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194557019 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 584) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194557019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194557019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557019 none O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 1, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 585) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194557019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194557019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557019 none O=C(N[C@@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 13, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 1, 1, 1, 5, 5, 1, 5, 5, 7, 48, 48, 48, 5, 5, 2, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194557019 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557019 Building ZINC000194557032 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194557032 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/586 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194557032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194557032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557032 none O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 1, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/587 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194557032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194557032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557032 none O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 2, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194557032 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 Building ZINC000194557032 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194557032 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 586) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194557032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194557032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557032 none O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 1, 5, 5] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 587) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194557032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194557032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194557032 none O=C(N[C@H](c1cccc(F)c1F)C(F)(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 15, 1, 15, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 6, 48, 48, 48, 5, 5, 2, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194557032 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194557032 Building ZINC000194699516 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194699516 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/588 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc21) `ZINC000194699516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194699516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194699516 none Cc1cccc2nc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/589 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2nc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc21) `ZINC000194699516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194699516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194699516 none Cc1cccc2nc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194699516 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 Building ZINC000194699516 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194699516 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 588) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc2nc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc21) `ZINC000194699516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194699516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194699516 none Cc1cccc2nc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 589) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc2nc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc21) `ZINC000194699516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194699516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194699516 none Cc1cccc2nc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/132203/xbs-8058115.45/working/building/ZINC000194699516 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194699516 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194699516 Building ZINC000194730604 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194730604 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/590 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194730604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194730604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194730604 none O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 8, 28, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 1, 2, 2, 21, 21, 21, 21, 28, 28, 38, 38, 38, 38, 38, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/591 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194730604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194730604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194730604 none O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 19, 19, 19, 19, 19, 8, 28, 37, 37, 32, 37, 37, 1, 1, 1, 2, 2, 1, 2, 2, 19, 19, 19, 19, 28, 28, 37, 37, 37, 37, 37, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194730604 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 Building ZINC000194730604 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194730604 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 590) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(N(CCC(F)(F)F)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194730604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194730604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194730604 none O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 8, 28, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 1, 2, 2, 21, 21, 21, 21, 28, 28, 38, 38, 38, 38, 38, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 591) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(N(CCC(F)(F)F)Cc1ccccc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194730604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194730604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000194730604 none O=C(N(CCC(F)(F)F)Cc1ccccc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 19, 19, 19, 19, 19, 8, 28, 37, 37, 32, 37, 37, 1, 1, 1, 2, 2, 1, 2, 2, 19, 19, 19, 19, 28, 28, 37, 37, 37, 37, 37, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000194730604 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000194730604 Building ZINC000434246723 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246723 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/592 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246723 none C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 19, 24, 24, 16, 16, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 24, 24, 19, 24, 24, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/593 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246723 none C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 18, 23, 23, 15, 15, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 23, 23, 18, 23, 23, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246723 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 Building ZINC000434246723 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246723 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 592) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246723 none C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 19, 24, 24, 16, 16, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 24, 24, 19, 24, 24, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 593) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246723 none C[C@@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 23, 18, 23, 23, 15, 15, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 23, 23, 18, 23, 23, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246723 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246723 Building ZINC000434246726 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246726 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/594 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246726 none C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 21, 23, 23, 17, 17, 8, 1, 8, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 17, 17, 17, 23, 23, 17, 23, 23, 17, 17, 17, 17, 6, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/595 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246726 none C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 24, 24, 18, 24, 24, 18, 18, 7, 1, 7, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 24, 24, 18, 24, 24, 18, 18, 18, 18, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246726 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 Building ZINC000434246726 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246726 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 594) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246726 none C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 21, 23, 23, 17, 17, 8, 1, 8, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 17, 17, 17, 23, 23, 17, 23, 23, 17, 17, 17, 17, 6, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 595) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246726 none C[C@H]1[C@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 24, 24, 18, 24, 24, 18, 18, 7, 1, 7, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 24, 24, 18, 24, 24, 18, 18, 18, 18, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246726 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246726 Building ZINC000434246727 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246727 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/596 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246727 none C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 27, 19, 27, 27, 19, 19, 9, 1, 9, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 19, 19, 19, 27, 27, 27, 27, 27, 19, 19, 19, 19, 5, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/597 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246727 none C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 9, 1, 9, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246727 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 Building ZINC000434246727 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246727 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 596) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246727 none C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 27, 19, 27, 27, 19, 19, 9, 1, 9, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 19, 19, 19, 27, 27, 27, 27, 27, 19, 19, 19, 19, 5, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 597) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246727 none C[C@@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 9, 1, 9, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246727 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246727 Building ZINC000434246729 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246729 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/598 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246729 none C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 10, 2, 10, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 24, 24, 18, 24, 24, 17, 17, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/599 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246729 none C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 24, 24, 17, 24, 24, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246729 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 Building ZINC000434246729 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000434246729 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 598) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000434246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246729 none C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 10, 2, 10, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 24, 24, 18, 24, 24, 17, 17, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 599) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000434246729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000434246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000434246729 none C[C@H]1[C@@H](c2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 24, 24, 17, 17, 9, 3, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 24, 24, 17, 24, 24, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000434246729 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000434246729 Building ZINC000357018355 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357018355 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/600 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC=C(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357018355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357018355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000357018355 none O=C(N1CCC=C(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 14, 14, 14, 14, 14, 29, 29, 14, 29, 29, 14, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 14, 14, 14, 14, 14, 29, 29, 23, 29, 29, 14, 14, 5, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/601 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC=C(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357018355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357018355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000357018355 none O=C(N1CCC=C(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 14, 14, 14, 14, 14, 27, 27, 14, 27, 27, 14, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 14, 14, 14, 14, 14, 27, 27, 14, 27, 27, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357018355 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 Building ZINC000357018355 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357018355 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 600) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC=C(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357018355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357018355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000357018355 none O=C(N1CCC=C(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 14, 14, 14, 14, 14, 29, 29, 14, 29, 29, 14, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 14, 14, 14, 14, 14, 29, 29, 23, 29, 29, 14, 14, 5, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 601) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC=C(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357018355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357018355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000357018355 none O=C(N1CCC=C(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 14, 14, 14, 14, 14, 27, 27, 14, 27, 27, 14, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 14, 14, 14, 14, 14, 27, 27, 14, 27, 27, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357018355 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357018355 Building ZINC000357206783 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357206783 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/602 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C) `ZINC000357206783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357206783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000357206783 none Cc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 8, 14, 14, 15, 15, 15, 15, 12, 15, 15, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/603 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C) `ZINC000357206783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357206783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000357206783 none Cc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 9, 8, 15, 15, 16, 16, 16, 16, 16, 16, 16, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 15, 15, 15, 15, 15, 15, 15] 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: 138 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357206783 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 Building ZINC000357206783 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357206783 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 602) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C) `ZINC000357206783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357206783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000357206783 none Cc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 15, 15, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 8, 14, 14, 15, 15, 15, 15, 12, 15, 15, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 603) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C) `ZINC000357206783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357206783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000357206783 none Cc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 9, 8, 15, 15, 16, 16, 16, 16, 16, 16, 16, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 15, 15, 15, 15, 15, 15, 15] 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: 138 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357206783 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357206783 Building ZINC000357277010 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357277010 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/604 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21) `ZINC000357277010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357277010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000357277010 none Cc1cccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/605 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21) `ZINC000357277010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357277010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000357277010 none Cc1cccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357277010 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 Building ZINC000357277010 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357277010 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 604) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21) `ZINC000357277010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357277010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000357277010 none Cc1cccc2c(CCNC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 605) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21) `ZINC000357277010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357277010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000357277010 none Cc1cccc2c(CCNC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357277010 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357277010 Building ZINC000357938700 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357938700 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/606 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357938700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357938700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000357938700 none Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 27, 27, 27, 27, 27, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 27, 27, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/607 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357938700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357938700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000357938700 none Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 24, 24, 24, 24, 24, 16, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 24, 24, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357938700 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 Building ZINC000357938700 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357938700 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 606) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357938700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357938700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000357938700 none Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 27, 27, 27, 27, 27, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 27, 27, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 607) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000357938700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357938700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000357938700 none Cc1ccc(c2ncc[nH]2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 24, 24, 24, 24, 24, 16, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 24, 24, 16, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000357938700 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000357938700 Building ZINC000358073384 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358073384 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/608 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1) `ZINC000358073384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358073384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000358073384 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 1, 5, 6, 6, 24, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 6, 6, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/609 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1) `ZINC000358073384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358073384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000358073384 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 47, 47, 47, 47, 47, 47, 47, 11, 11, 11, 6, 6, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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]) total number of confs: 133 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358073384 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 Building ZINC000358073384 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358073384 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 608) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1) `ZINC000358073384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358073384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000358073384 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 6, 6, 1, 5, 6, 6, 24, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 6, 6, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 609) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1) `ZINC000358073384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358073384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000358073384 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 47, 47, 47, 47, 47, 47, 47, 11, 11, 11, 6, 6, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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]) total number of confs: 133 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358073384 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358073384 Building ZINC000435735426 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435735426 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/610 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1) `ZINC000435735426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435735426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000435735426 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/611 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1) `ZINC000435735426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435735426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000435735426 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 4, 15, 15, 15, 15, 15, 50, 50, 46, 50, 50, 50, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 15, 15, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000435735426 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 Building ZINC000435735426 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000435735426 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 610) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1) `ZINC000435735426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000435735426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000435735426 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 611) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1) `ZINC000435735426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000435735426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000435735426 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3cccc(Cl)c3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 4, 15, 15, 15, 15, 15, 50, 50, 46, 50, 50, 50, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 50, 50, 50, 50, 15, 15, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000435735426 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000435735426 Building ZINC000358499261 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358499261 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/612 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1) `ZINC000358499261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358499261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000358499261 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/613 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1) `ZINC000358499261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358499261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000358499261 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358499261 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 Building ZINC000358499261 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358499261 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 612) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1) `ZINC000358499261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358499261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000358499261 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 613) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1) `ZINC000358499261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358499261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000358499261 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358499261 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358499261 Building ZINC000358664810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/614 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/615 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/616 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/616' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/617 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/617' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 Building ZINC000358664810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 614) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 615) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 616) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 617) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 Building ZINC000358664810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 614) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 615) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 616) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 617) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 Building ZINC000358664810 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664810 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 614) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 615) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 15, 2, 16, 1, 1, 1, 9, 9, 14, 14, 9, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 616) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 617) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664810.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664810 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664810 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664810 Building ZINC000358664817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/618 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/619 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/620 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/620' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/621 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/621' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 Building ZINC000358664817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 618) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 619) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 620) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 621) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 Building ZINC000358664817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 618) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 619) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 620) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 621) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 Building ZINC000358664817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000358664817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 618) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 619) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 2, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7] 44 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]) total number of confs: 46 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `2' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 2 (index: 620) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `3' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 3 (index: 621) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358664817.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000358664817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000358664817 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358664817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 2: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/2.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/0.* 3: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817/3.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358664817 Building ZINC000358717328 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358717328 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/622 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C) `ZINC000358717328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358717328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000358717328 none Cc1oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/623 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C) `ZINC000358717328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358717328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000358717328 none Cc1oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358717328 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 Building ZINC000358717328 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358717328 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 622) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C) `ZINC000358717328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358717328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000358717328 none Cc1oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 623) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C) `ZINC000358717328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358717328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000358717328 none Cc1oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358717328 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358717328 Building ZINC000436166625 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436166625 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/624 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCC2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000436166625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436166625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000436166625 none O=C(Nc1nc(C2CCC2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 26, 26, 26, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/625 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCC2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000436166625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436166625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000436166625 none O=C(Nc1nc(C2CCC2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 29, 29, 29, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436166625 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 Building ZINC000436166625 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436166625 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 624) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(C2CCC2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000436166625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436166625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000436166625 none O=C(Nc1nc(C2CCC2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 26, 26, 26, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 625) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc(C2CCC2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000436166625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436166625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000436166625 none O=C(Nc1nc(C2CCC2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 29, 29, 29, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436166625 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436166625 Building ZINC000358881329 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358881329 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/626 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358881329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358881329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000358881329 none O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 8, 12, 12, 12, 12, 28, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/627 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358881329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358881329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000358881329 none O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 10, 12, 12, 12, 12, 29, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358881329 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 Building ZINC000358881329 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358881329 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 626) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358881329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358881329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000358881329 none O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 8, 12, 12, 12, 12, 28, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 627) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000358881329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358881329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000358881329 none O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 10, 12, 12, 12, 12, 29, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358881329 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358881329 Building ZINC000358969133 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358969133 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/628 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12) `ZINC000358969133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358969133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000358969133 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/629 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12) `ZINC000358969133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358969133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000358969133 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358969133 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 Building ZINC000358969133 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000358969133 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 628) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12) `ZINC000358969133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000358969133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000358969133 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 629) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12) `ZINC000358969133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000358969133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000358969133 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000358969133 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000358969133 Building ZINC000359061866 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359061866 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/630 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359061866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061866 none O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 9, 30, 30, 30, 30, 30, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 30, 30, 30, 30, 30, 29, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/631 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359061866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061866 none O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 5, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 28, 28, 28, 28, 28, 28, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359061866 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 Building ZINC000359061866 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359061866 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 630) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359061866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061866 none O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 9, 30, 30, 30, 30, 30, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 30, 30, 30, 30, 30, 29, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 631) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359061866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061866 none O=C(Nc1ccc([C@@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 5, 28, 28, 28, 28, 28, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 28, 28, 28, 28, 28, 28, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359061866 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061866 Building ZINC000359061871 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359061871 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/632 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359061871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061871 none O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 5, 30, 30, 31, 31, 30, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 31, 31, 31, 31, 30, 31, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/633 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359061871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061871 none O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 5, 30, 30, 30, 30, 30, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 30, 30, 30, 30, 30, 30, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359061871 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 Building ZINC000359061871 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359061871 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 632) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359061871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061871 none O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 5, 30, 30, 31, 31, 30, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 31, 31, 31, 31, 30, 31, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 633) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359061871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359061871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000359061871 none O=C(Nc1ccc([C@H]2CCOC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 7, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 5, 30, 30, 30, 30, 30, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 30, 30, 30, 30, 30, 30, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359061871 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359061871 Building ZINC000359069226 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069226 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/634 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1) `ZINC000359069226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069226 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/635 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1) `ZINC000359069226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069226 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 3, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 46, 46, 46] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069226 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 Building ZINC000359069226 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069226 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 634) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1) `ZINC000359069226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069226 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 635) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1) `ZINC000359069226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069226 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 3, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 46, 46, 46] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069226 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069226 Building ZINC000359069227 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069227 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/636 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1) `ZINC000359069227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069227 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 1, 8, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/637 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1) `ZINC000359069227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069227 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069227 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 Building ZINC000359069227 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069227 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 636) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1) `ZINC000359069227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069227 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 1, 8, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 637) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1) `ZINC000359069227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069227 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069227 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069227 Building ZINC000359069228 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069228 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/638 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1) `ZINC000359069228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069228 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 4, 4, 4, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/639 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1) `ZINC000359069228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069228 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 1, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069228 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 Building ZINC000359069228 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069228 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 638) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1) `ZINC000359069228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069228 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 4, 4, 4, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 639) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1) `ZINC000359069228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069228 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 1, 8, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069228 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069228 Building ZINC000359069229 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069229 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/640 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1) `ZINC000359069229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069229 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 3, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 46, 46, 46] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/641 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1) `ZINC000359069229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069229 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069229 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 Building ZINC000359069229 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359069229 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 640) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1) `ZINC000359069229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359069229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069229 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 3, 3, 1, 1, 1, 3, 15, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 46, 46, 46] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 641) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1) `ZINC000359069229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359069229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359069229 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C)C[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359069229 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359069229 Building ZINC000359098188 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359098188 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/642 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(F)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359098188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359098188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359098188 none CSc1cccc(F)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 23, 23, 20, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 23, 23, 23, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/643 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(F)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359098188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359098188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359098188 none CSc1cccc(F)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 21, 21, 21, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 21, 21, 21, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359098188 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 Building ZINC000359098188 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359098188 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 642) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSc1cccc(F)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359098188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359098188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359098188 none CSc1cccc(F)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 23, 23, 20, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 23, 23, 23, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 643) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSc1cccc(F)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359098188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359098188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359098188 none CSc1cccc(F)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 21, 21, 21, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 21, 21, 21, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359098188 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359098188 Building ZINC000436706144 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706144 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/644 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706144 none CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/645 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706144 none CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 50, 50, 50, 50, 50, 37, 37, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706144 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 Building ZINC000436706144 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706144 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 644) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706144 none CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 645) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706144 none CCc1ccc([C@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 37, 50, 50, 50, 50, 50, 37, 37, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 6, 3, 3] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706144 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706144 Building ZINC000436706145 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706145 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/646 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706145 none CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 4, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 50, 50, 50, 50, 50, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 4, 2, 2] 100 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]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/647 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706145 none CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 3, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3] 100 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706145 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 Building ZINC000436706145 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706145 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 646) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706145 none CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 4, 12, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 50, 50, 50, 50, 50, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 4, 2, 2] 100 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]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 647) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706145 none CCc1ccc([C@@H]2C[C@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 3, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 50, 50, 50, 50, 50, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3] 100 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706145 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706145 Building ZINC000436706146 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706146 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/648 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706146 none CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 35, 35, 35, 35, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 50, 50, 50, 50, 50, 35, 35, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 6, 3, 3] 100 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/649 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706146 none CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3] 100 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706146 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 Building ZINC000436706146 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706146 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 648) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706146 none CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 35, 35, 35, 35, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 50, 50, 50, 50, 50, 35, 35, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 6, 3, 3] 100 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 649) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706146 none CCc1ccc([C@@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3] 100 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706146 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706146 Building ZINC000436706147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/650 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706147 none CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3] 100 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/651 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706147 none CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 4, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 6, 3, 3] 100 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]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 Building ZINC000436706147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000436706147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 650) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000436706147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706147 none CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3] 100 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 651) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1) `ZINC000436706147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000436706147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000436706147 none CCc1ccc([C@H]2C[C@@H](C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 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: [50, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 4, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 6, 3, 3] 100 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]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000436706147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000436706147 Building ZINC000359397159 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359397159 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/652 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccn2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359397159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359397159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000359397159 none O=C(Nc1ncc(c2ccccn2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 31, 31, 31, 31, 31, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/653 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccn2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359397159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359397159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000359397159 none O=C(Nc1ncc(c2ccccn2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 28, 28, 28, 28, 28, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359397159 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 Building ZINC000359397159 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359397159 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 652) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ncc(c2ccccn2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359397159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359397159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000359397159 none O=C(Nc1ncc(c2ccccn2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 31, 31, 31, 31, 31, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 653) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ncc(c2ccccn2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359397159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359397159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000359397159 none O=C(Nc1ncc(c2ccccn2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 28, 28, 28, 28, 28, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359397159 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359397159 Building ZINC000359453509 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359453509 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/654 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359453509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453509 none C[C@@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 34, 34, 34, 34, 34, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 6, 6, 6, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/655 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359453509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453509 none C[C@@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 35, 35, 35, 35, 35, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 13, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359453509 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 Building ZINC000359453509 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359453509 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 654) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359453509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453509 none C[C@@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 34, 34, 34, 34, 34, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 6, 6, 6, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 655) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359453509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453509 none C[C@@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 35, 35, 35, 35, 35, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 13, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359453509 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453509 Building ZINC000359453510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359453510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/656 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359453510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453510 none C[C@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 16, 32, 32, 32, 32, 32, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/657 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359453510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453510 none C[C@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 36, 36, 36, 36, 36, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 6, 6, 6, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359453510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 Building ZINC000359453510 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359453510 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 656) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359453510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453510 none C[C@H](CCC1CCCCC1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 16, 32, 32, 32, 32, 32, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 657) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359453510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359453510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000359453510 none C[C@H](CCC1CCCCC1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 7, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 36, 36, 36, 36, 36, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 6, 6, 6, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359453510 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359453510 Building ZINC000359492398 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359492398 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/658 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12) `ZINC000359492398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359492398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359492398 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/659 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12) `ZINC000359492398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359492398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359492398 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359492398 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 Building ZINC000359492398 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359492398 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 658) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12) `ZINC000359492398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359492398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359492398 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 659) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12) `ZINC000359492398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359492398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000359492398 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359492398 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359492398 Building ZINC000359542792 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359542792 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/660 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1coc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12) `ZINC000359542792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359542792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000359542792 none Cc1coc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 16, 16, 16, 16, 16, 16, 16, 16, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/661 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1coc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12) `ZINC000359542792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359542792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000359542792 none Cc1coc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 16, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359542792 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 Building ZINC000359542792 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359542792 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 660) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1coc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12) `ZINC000359542792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359542792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000359542792 none Cc1coc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 16, 16, 16, 16, 16, 16, 16, 16, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 661) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1coc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12) `ZINC000359542792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359542792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000359542792 none Cc1coc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 16, 16, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 16, 16, 16, 16, 16, 16, 16, 16, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359542792 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359542792 Building ZINC000359737318 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359737318 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/662 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359737318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359737318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359737318 none O=C(Nc1ccc(OCC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 2, 15, 24, 37, 37, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 24, 24, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/663 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359737318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359737318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359737318 none O=C(Nc1ccc(OCC(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 4, 6, 21, 25, 37, 37, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 25, 25, 37, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359737318 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 Building ZINC000359737318 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359737318 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 662) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(OCC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359737318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359737318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359737318 none O=C(Nc1ccc(OCC(F)F)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 2, 15, 24, 37, 37, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 24, 24, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 663) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc(OCC(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000359737318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359737318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000359737318 none O=C(Nc1ccc(OCC(F)F)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 4, 6, 21, 25, 37, 37, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 25, 25, 37, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359737318 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359737318 Building ZINC000437273279 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437273279 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/664 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1) `ZINC000437273279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437273279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437273279 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/665 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1) `ZINC000437273279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437273279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437273279 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437273279 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 Building ZINC000437273279 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437273279 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 664) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1) `ZINC000437273279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437273279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437273279 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 665) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1) `ZINC000437273279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437273279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437273279 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437273279 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437273279 Building ZINC000359978391 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359978391 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/666 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359978391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359978391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000359978391 none CC(C)(C)Oc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 8, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/667 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359978391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359978391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000359978391 none CC(C)(C)Oc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359978391 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 Building ZINC000359978391 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000359978391 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 666) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359978391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000359978391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000359978391 none CC(C)(C)Oc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 19, 8, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 4, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 667) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000359978391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000359978391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000359978391 none CC(C)(C)Oc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000359978391 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000359978391 Building ZINC000437422648 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437422648 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/668 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437422648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437422648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437422648 none O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/669 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437422648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437422648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437422648 none O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 28, 28, 28, 28, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437422648 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 Building ZINC000437422648 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437422648 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 668) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437422648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437422648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437422648 none O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 28, 28, 28, 28, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 669) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437422648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437422648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437422648 none O=C(N[C@H]1C[C@H](c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 28, 28, 28, 28, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437422648 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437422648 Building ZINC000437451629 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437451629 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/670 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437451629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437451629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437451629 none O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 31, 31, 13, 31, 31, 31, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 31, 31, 27, 31, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/671 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437451629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437451629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437451629 none O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 11, 11, 11, 11, 11, 31, 31, 11, 31, 31, 31, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 30, 31, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437451629 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 Building ZINC000437451629 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437451629 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 670) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437451629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437451629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437451629 none O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 31, 31, 13, 31, 31, 31, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 31, 31, 27, 31, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 671) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000437451629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437451629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000437451629 none O=C(N[C@H]1C[C@H](c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 11, 11, 11, 11, 11, 31, 31, 11, 31, 31, 31, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 30, 31, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437451629 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437451629 Building ZINC000437458109 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437458109 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/672 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)C1) `ZINC000437458109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437458109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000437458109 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/673 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)C1) `ZINC000437458109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437458109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000437458109 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 50, 50, 39, 50, 50, 50, 14, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 50, 50, 50, 50, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437458109 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 Building ZINC000437458109 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000437458109 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 672) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)C1) `ZINC000437458109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000437458109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000437458109 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 673) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)C1) `ZINC000437458109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000437458109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000437458109 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(Cl)c2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 50, 50, 39, 50, 50, 50, 14, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 50, 50, 50, 50, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000437458109 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000437458109 Building ZINC000360107524 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360107524 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/674 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)ccc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360107524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360107524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360107524 none O=C(N1CCc2cc(Cl)ccc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/675 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)ccc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360107524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360107524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360107524 none O=C(N1CCc2cc(Cl)ccc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360107524 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 Building ZINC000360107524 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360107524 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 674) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)ccc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360107524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360107524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360107524 none O=C(N1CCc2cc(Cl)ccc2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 675) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Cl)ccc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360107524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360107524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360107524 none O=C(N1CCc2cc(Cl)ccc2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 9, 9, 9, 9, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360107524 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360107524 Building ZINC000360339821 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360339821 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/676 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cccc(Cl)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360339821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360339821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000360339821 none O=C(N1Cc2cccc(Cl)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/677 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cccc(Cl)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360339821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360339821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000360339821 none O=C(N1Cc2cccc(Cl)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360339821 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 Building ZINC000360339821 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360339821 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 676) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1Cc2cccc(Cl)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360339821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360339821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000360339821 none O=C(N1Cc2cccc(Cl)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 677) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1Cc2cccc(Cl)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360339821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360339821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000360339821 none O=C(N1Cc2cccc(Cl)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360339821 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360339821 Building ZINC000438020943 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438020943 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/678 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)cn1) `ZINC000438020943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438020943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000438020943 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)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', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 4, 14, 27, 27, 27, 4, 11, 11, 4, 11, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 9, 9, 27, 27, 27, 27, 27, 27, 27, 11, 11, 4, 11, 11, 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]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/679 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)cn1) `ZINC000438020943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438020943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000438020943 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)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', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 4, 13, 24, 24, 24, 4, 11, 11, 4, 11, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 24, 24, 24, 24, 24, 24, 24, 11, 11, 4, 11, 11, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000438020943 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 Building ZINC000438020943 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438020943 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 678) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)cn1) `ZINC000438020943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438020943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000438020943 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)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', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 4, 14, 27, 27, 27, 4, 11, 11, 4, 11, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 9, 9, 27, 27, 27, 27, 27, 27, 27, 11, 11, 4, 11, 11, 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]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 679) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)cn1) `ZINC000438020943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438020943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000438020943 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC2CCC2)c2ccccc2)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', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 4, 13, 24, 24, 24, 4, 11, 11, 4, 11, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 24, 24, 24, 24, 24, 24, 24, 11, 11, 4, 11, 11, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000438020943 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438020943 Building ZINC000360627054 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360627054 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/680 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2ccc(O)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360627054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360627054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360627054 none O=C(Nc1cccc2ccc(O)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 21, 21, 21, 21, 21, 42, 21, 10, 10, 10, 10, 10, 10, 10, 10, 10] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/681 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2ccc(O)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360627054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360627054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360627054 none O=C(Nc1cccc2ccc(O)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 21, 21, 21, 21, 21, 42, 21, 10, 10, 10, 10, 10, 10, 10, 10, 10] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360627054 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 Building ZINC000360627054 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360627054 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 680) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc2ccc(O)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360627054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360627054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360627054 none O=C(Nc1cccc2ccc(O)cc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 21, 21, 21, 21, 21, 42, 21, 10, 10, 10, 10, 10, 10, 10, 10, 10] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 681) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1cccc2ccc(O)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000360627054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360627054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000360627054 none O=C(Nc1cccc2ccc(O)cc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 21, 21, 21, 21, 21, 42, 21, 10, 10, 10, 10, 10, 10, 10, 10, 10] 100 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360627054 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360627054 Building ZINC000438384637 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438384637 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/682 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000438384637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438384637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000438384637 none CSCc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 11, 16, 13, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 16, 27, 27, 27, 27, 27, 11, 16, 16, 7, 7, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [34, 8, 9, 10, 11, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/683 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000438384637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438384637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000438384637 none CSCc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 17, 11, 17, 14, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 17, 29, 29, 29, 28, 28, 11, 17, 17, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17] 50 rigid atoms, others: [34, 8, 9, 10, 11, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000438384637 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 Building ZINC000438384637 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000438384637 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 682) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSCc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000438384637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000438384637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000438384637 none CSCc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 11, 16, 13, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 16, 27, 27, 27, 27, 27, 11, 16, 16, 7, 7, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [34, 8, 9, 10, 11, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 683) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSCc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000438384637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000438384637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000438384637 none CSCc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 17, 17, 11, 17, 14, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 17, 29, 29, 29, 28, 28, 11, 17, 17, 7, 7, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17] 50 rigid atoms, others: [34, 8, 9, 10, 11, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000438384637 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000438384637 Building ZINC000360896465 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360896465 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/684 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)c2)cn1) `ZINC000360896465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360896465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000360896465 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 2, 8, 8, 31, 31, 31, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 8, 8, 2, 31, 31, 31, 31, 31, 31, 31, 8, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/685 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)c2)cn1) `ZINC000360896465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360896465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000360896465 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 8, 8, 2, 8, 8, 33, 33, 33, 8, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 8, 8, 6, 33, 33, 33, 33, 33, 33, 33, 8, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360896465 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 Building ZINC000360896465 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000360896465 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 684) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)c2)cn1) `ZINC000360896465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000360896465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000360896465 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 2, 8, 8, 31, 31, 31, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 8, 8, 2, 31, 31, 31, 31, 31, 31, 31, 8, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 685) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)c2)cn1) `ZINC000360896465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000360896465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000360896465 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CCC3)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', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 8, 8, 2, 8, 8, 33, 33, 33, 8, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 8, 8, 6, 33, 33, 33, 33, 33, 33, 33, 8, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000360896465 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000360896465 Building ZINC000361196609 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361196609 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/686 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCn1nc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000361196609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361196609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000361196609 none CCCCCn1nc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 7, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/687 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCn1nc(C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000361196609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361196609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000361196609 none CCCCCn1nc(C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 7, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361196609 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 Building ZINC000361196609 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361196609 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 686) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCCn1nc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000361196609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361196609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000361196609 none CCCCCn1nc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 7, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 687) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCCn1nc(C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000361196609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361196609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000361196609 none CCCCCn1nc(C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 7, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 20, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361196609 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361196609 Building ZINC000361353718 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361353718 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/688 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361353718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353718 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 15, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/689 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361353718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353718 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361353718 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 Building ZINC000361353718 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361353718 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 688) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361353718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353718 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 15, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 689) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361353718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353718 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 14, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361353718 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353718 Building ZINC000361353719 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361353719 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/690 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361353719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353719 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/691 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361353719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353719 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 13, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361353719 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 Building ZINC000361353719 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000361353719 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 690) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000361353719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353719 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 691) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000361353719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000361353719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000361353719 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 1, 13, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000361353719 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000361353719 Building ZINC000439183848 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439183848 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/692 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F) `ZINC000439183848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000439183848 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 28, 28, 9, 28, 28, 28, 28, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/693 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F) `ZINC000439183848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000439183848 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000439183848 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 Building ZINC000439183848 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439183848 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 692) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F) `ZINC000439183848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000439183848 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 28, 28, 9, 28, 28, 28, 28, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 693) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F) `ZINC000439183848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000439183848 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000439183848 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439183848 Building ZINC000439220631 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439220631 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/694 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)c(C(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000439220631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439220631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000439220631 none Cc1cc(O)c(C(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 4, 4, 14, 14, 19, 19, 14, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 14, 14, 14, 14, 28, 19, 19, 19, 19, 19, 19, 19, 14, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/695 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)c(C(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000439220631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439220631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000439220631 none Cc1cc(O)c(C(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 8, 12, 12, 15, 15, 12, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 11, 12, 12, 12, 12, 24, 15, 15, 15, 15, 15, 15, 15, 12, 4, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000439220631 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 Building ZINC000439220631 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000439220631 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 694) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(O)c(C(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000439220631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000439220631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000439220631 none Cc1cc(O)c(C(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 4, 4, 14, 14, 19, 19, 14, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 14, 14, 14, 14, 28, 19, 19, 19, 19, 19, 19, 19, 14, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 695) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(O)c(C(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000439220631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000439220631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000439220631 none Cc1cc(O)c(C(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 8, 12, 12, 15, 15, 12, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 11, 12, 12, 12, 12, 24, 15, 15, 15, 15, 15, 15, 15, 12, 4, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000439220631 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000439220631 Building ZINC000362015323 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362015323 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/696 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362015323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015323 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 30, 30, 30, 30, 30, 30, 18, 18, 18, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/697 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362015323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015323 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 27, 28, 28, 27, 28, 28, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362015323 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 Building ZINC000362015323 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362015323 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 696) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362015323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015323 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 30, 30, 30, 30, 30, 30, 18, 18, 18, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 697) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362015323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015323 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 27, 28, 28, 27, 28, 28, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362015323 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015323 Building ZINC000362015330 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362015330 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/698 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362015330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015330 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 20, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 20, 30, 30, 30, 30, 30, 30, 20, 20, 20, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/699 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362015330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015330 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362015330 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 Building ZINC000362015330 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362015330 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 698) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362015330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015330 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 20, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 20, 30, 30, 30, 30, 30, 30, 20, 20, 20, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 699) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1) `ZINC000362015330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362015330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000362015330 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Sc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362015330 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362015330 Building ZINC000510064543 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510064543 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/700 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510064543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000510064543 none CCCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 11, 5, 11, 21, 25, 25, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 27, 27, 27, 27, 27, 20, 20, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4] 47 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/701 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510064543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000510064543 none CCCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 10, 4, 10, 20, 23, 23, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 19, 19, 20, 20, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5] 42 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510064543 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 Building ZINC000510064543 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510064543 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 700) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510064543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000510064543 none CCCN(CC(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 11, 5, 11, 21, 25, 25, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 27, 27, 27, 27, 27, 20, 20, 21, 21, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4] 47 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 701) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510064543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000510064543 none CCCN(CC(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 10, 4, 10, 20, 23, 23, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 26, 26, 26, 26, 26, 19, 19, 20, 20, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5] 42 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510064543 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510064543 Building ZINC000362188199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362188199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/702 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(F)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000362188199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362188199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000362188199 none CCSc1cccc(F)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 17, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 26, 26, 26, 26, 26, 6, 6, 6, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/703 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(F)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000362188199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362188199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000362188199 none CCSc1cccc(F)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 27, 27, 27, 27, 27, 6, 6, 6, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362188199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 Building ZINC000362188199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362188199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 702) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(F)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000362188199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362188199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000362188199 none CCSc1cccc(F)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 17, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 26, 26, 26, 26, 26, 6, 6, 6, 4, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 703) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(F)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000362188199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362188199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000362188199 none CCSc1cccc(F)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 27, 27, 27, 27, 27, 6, 6, 6, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362188199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362188199 Building ZINC000510165452 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510165452 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/704 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510165452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510165452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000510165452 none O=C(NCCC1=CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 46, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/705 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510165452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510165452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000510165452 none O=C(NCCC1=CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 46, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510165452 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 Building ZINC000510165452 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510165452 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 704) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCCC1=CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510165452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510165452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000510165452 none O=C(NCCC1=CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 46, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 705) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCCC1=CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000510165452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510165452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000510165452 none O=C(NCCC1=CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 40, 46, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 40, 40, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 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]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510165452 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510165452 Building ZINC000362264916 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362264916 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/706 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/706' -> `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(c3ccccn3)cc2)cn1) `ZINC000362264916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362264916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000362264916 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 24, 24, 24, 24, 24, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 6, 6, 23, 24, 26, 24, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/707 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/707' -> `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(c3ccccn3)cc2)cn1) `ZINC000362264916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362264916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000362264916 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 4, 4, 26, 26, 26, 26, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362264916 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 Building ZINC000362264916 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362264916 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 706) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)cc2)cn1) `ZINC000362264916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362264916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000362264916 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 24, 24, 24, 24, 24, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 6, 6, 23, 24, 26, 24, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 707) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)cc2)cn1) `ZINC000362264916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362264916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000362264916 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccccn3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 4, 4, 2, 2, 26, 26, 26, 26, 26, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 4, 4, 26, 26, 26, 26, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362264916 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362264916 Building ZINC000362281991 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362281991 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/708 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362281991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362281991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000362281991 none O=C(N(CC(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 21, 21, 6, 15, 15, 6, 15, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 21, 15, 15, 7, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/709 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362281991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362281991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000362281991 none O=C(N(CC(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 20, 20, 6, 15, 15, 6, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 20, 15, 15, 9, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362281991 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 Building ZINC000362281991 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362281991 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 708) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(CC(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362281991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362281991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000362281991 none O=C(N(CC(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 21, 21, 6, 15, 15, 6, 15, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 21, 15, 15, 7, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 709) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(CC(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362281991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362281991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000362281991 none O=C(N(CC(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 11, 20, 20, 6, 15, 15, 6, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 20, 15, 15, 9, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362281991 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362281991 Building ZINC000362318653 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362318653 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/710 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(F)(F)F)ncc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362318653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362318653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362318653 none Cc1cc(C(F)(F)F)ncc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/711 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(F)(F)F)ncc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362318653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362318653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362318653 none Cc1cc(C(F)(F)F)ncc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362318653 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 Building ZINC000362318653 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362318653 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 710) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(C(F)(F)F)ncc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362318653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362318653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362318653 none Cc1cc(C(F)(F)F)ncc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 711) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(C(F)(F)F)ncc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362318653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362318653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000362318653 none Cc1cc(C(F)(F)F)ncc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362318653 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362318653 Building ZINC000510396719 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510396719 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/712 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1) `ZINC000510396719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510396719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000510396719 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 30, 30, 30, 30, 14, 14, 14, 14, 14, 14, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/713 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1) `ZINC000510396719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510396719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000510396719 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 31, 31, 31, 31, 14, 14, 14, 14, 14, 14, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510396719 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 Building ZINC000510396719 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510396719 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 712) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1) `ZINC000510396719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510396719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000510396719 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 30, 30, 30, 30, 14, 14, 14, 14, 14, 14, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 713) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1) `ZINC000510396719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510396719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000510396719 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 31, 31, 31, 31, 14, 14, 14, 14, 14, 14, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510396719 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510396719 Building ZINC000362521324 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362521324 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/714 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000362521324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362521324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000362521324 none CCCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 27, 27, 27, 27, 27, 24, 24, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/715 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000362521324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362521324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000362521324 none CCCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 26, 26, 26, 26, 26, 23, 23, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362521324 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 Building ZINC000362521324 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362521324 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 714) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000362521324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362521324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000362521324 none CCCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 27, 27, 27, 27, 27, 24, 24, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 715) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000362521324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362521324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000362521324 none CCCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 26, 26, 26, 26, 26, 23, 23, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362521324 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362521324 Building ZINC000440839843 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839843 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/716 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839843 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 14, 14, 14, 14, 11, 3, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 14, 14] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/717 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839843 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839843 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 Building ZINC000440839843 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839843 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 716) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839843 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 14, 14, 14, 14, 11, 3, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 14, 14] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 717) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839843 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 10, 3, 10, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839843 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839843 Building ZINC000440839844 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839844 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/718 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839844 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [15, 15, 15, 15, 15, 11, 3, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 15, 15] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/719 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839844 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 8, 2, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839844 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 Building ZINC000440839844 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839844 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 718) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839844 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [15, 15, 15, 15, 15, 11, 3, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 15, 15] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 719) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839844 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 8, 2, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839844 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839844 Building ZINC000440839845 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839845 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/720 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839845 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/721 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839845 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 15, 15, 15, 33, 33, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 5, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839845 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 Building ZINC000440839845 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839845 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 720) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839845 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 721) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1) `ZINC000440839845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839845 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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: [15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 8, 15, 15, 15, 33, 33, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 5, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839845 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839845 Building ZINC000440839846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/722 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839846 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 37, 37, 37, 37, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 13, 13] 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/723 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839846 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 Building ZINC000440839846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000440839846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 722) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000440839846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839846 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 37, 37, 37, 37, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 13, 13] 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 723) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1) `ZINC000440839846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000440839846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000440839846 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 13, 13, 13, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 13, 6, 8, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 13, 13] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000440839846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000440839846 Building ZINC000362653041 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362653041 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/724 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(F)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362653041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362653041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000362653041 none CSc1ccc(F)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 29, 29, 29, 29, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 29, 29, 29, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/725 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(F)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362653041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362653041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000362653041 none CSc1ccc(F)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 27, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362653041 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 Building ZINC000362653041 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000362653041 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 724) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSc1ccc(F)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362653041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000362653041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000362653041 none CSc1ccc(F)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 29, 29, 29, 29, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 29, 29, 29, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 725) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSc1ccc(F)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000362653041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000362653041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000362653041 none CSc1ccc(F)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 27, 27, 27, 27, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000362653041 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000362653041 Building ZINC000510744587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510744587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/726 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000510744587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510744587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000510744587 none COc1ccc(Cl)cc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 7, 26, 26, 26, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 26, 15, 26, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/727 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000510744587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510744587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000510744587 none COc1ccc(Cl)cc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 8, 26, 26, 26, 6, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 26, 12, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510744587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 Building ZINC000510744587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000510744587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 726) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)cc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000510744587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000510744587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000510744587 none COc1ccc(Cl)cc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 7, 26, 26, 26, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 26, 15, 26, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 727) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(Cl)cc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000510744587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000510744587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000510744587 none COc1ccc(Cl)cc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 8, 26, 26, 26, 6, 4, 6, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 26, 12, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000510744587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000510744587 Building ZINC000441490015 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441490015 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/728 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl) `ZINC000441490015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441490015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000441490015 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 11, 23, 23, 18, 23, 23, 23, 13, 13, 13, 13, 13, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 18, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/729 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl) `ZINC000441490015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441490015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000441490015 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 9, 19, 19, 16, 19, 19, 19, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 19, 19, 16, 19] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000441490015 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 Building ZINC000441490015 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000441490015 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 728) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl) `ZINC000441490015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000441490015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000441490015 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 11, 23, 23, 18, 23, 23, 23, 13, 13, 13, 13, 13, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 23, 23, 18, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 729) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl) `ZINC000441490015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000441490015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000441490015 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 5, 9, 19, 19, 16, 19, 19, 19, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 19, 19, 16, 19] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000441490015 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000441490015 Building ZINC000511312405 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511312405 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/730 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(F)(F)F)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000511312405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511312405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000511312405 none O=C(NC1(C(F)(F)F)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/731 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(C(F)(F)F)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000511312405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511312405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000511312405 none O=C(NC1(C(F)(F)F)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000511312405 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 Building ZINC000511312405 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511312405 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 730) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1(C(F)(F)F)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000511312405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511312405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000511312405 none O=C(NC1(C(F)(F)F)CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 731) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NC1(C(F)(F)F)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000511312405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511312405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000511312405 none O=C(NC1(C(F)(F)F)CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000511312405 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000511312405 Building ZINC000442425551 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442425551 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/732 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl) `ZINC000442425551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442425551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000442425551 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 16, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 11, 13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/733 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl) `ZINC000442425551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442425551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000442425551 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 16, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 11, 14, 14, 14, 4, 4, 14, 14, 14, 14, 4, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 14, 14, 14, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000442425551 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 Building ZINC000442425551 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000442425551 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 732) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl) `ZINC000442425551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000442425551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000442425551 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 16, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 11, 13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 733) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl) `ZINC000442425551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000442425551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000442425551 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(C)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 16, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 11, 14, 14, 14, 4, 4, 14, 14, 14, 14, 4, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 14, 14, 14, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000442425551 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000442425551 Building ZINC000513335087 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513335087 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/734 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F) `ZINC000513335087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513335087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000513335087 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 21, 24, 24, 10, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/735 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F) `ZINC000513335087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513335087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000513335087 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 22, 26, 26, 10, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513335087 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 Building ZINC000513335087 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513335087 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 734) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F) `ZINC000513335087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513335087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000513335087 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 21, 24, 24, 10, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 24] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 735) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F) `ZINC000513335087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513335087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000513335087 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 22, 26, 26, 10, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513335087 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513335087 Building ZINC000513553527 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513553527 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/736 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513553527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553527 none Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 30, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 30, 30, 30, 30, 24, 30, 30, 24, 24, 13, 13, 13, 13, 13, 13, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/737 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513553527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553527 none Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 28, 28, 19, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 28, 28, 28, 28, 19, 28, 28, 19, 19, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513553527 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 Building ZINC000513553527 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513553527 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 736) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513553527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553527 none Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 30, 30, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 30, 30, 30, 30, 24, 30, 30, 24, 24, 13, 13, 13, 13, 13, 13, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 737) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513553527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553527 none Cc1ccccc1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 28, 28, 19, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 28, 28, 28, 28, 19, 28, 28, 19, 19, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513553527 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553527 Building ZINC000513553529 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513553529 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/738 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513553529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553529 none Cc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 29, 20, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 29, 29, 29, 29, 20, 29, 29, 20, 20, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10] 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: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/739 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513553529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553529 none Cc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 30, 30, 23, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 23, 30, 30, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513553529 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 Building ZINC000513553529 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513553529 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 738) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513553529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553529 none Cc1ccccc1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 29, 20, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 29, 29, 29, 29, 20, 29, 29, 20, 20, 11, 11, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10] 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: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 739) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000513553529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513553529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000513553529 none Cc1ccccc1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 30, 30, 23, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 23, 30, 30, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000513553529 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000513553529 Building ZINC000446302735 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000446302735 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/740 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1) `ZINC000446302735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000446302735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000446302735 none CC(C)CC1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/741 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1) `ZINC000446302735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000446302735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000446302735 none CC(C)CC1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000446302735 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 Building ZINC000446302735 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000446302735 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 740) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)CC1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1) `ZINC000446302735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000446302735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000446302735 none CC(C)CC1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 741) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)CC1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1) `ZINC000446302735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000446302735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000446302735 none CC(C)CC1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000446302735 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000446302735 Building ZINC000447713955 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447713955 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/742 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl) `ZINC000447713955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447713955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447713955 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 30, 30, 30, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/743 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl) `ZINC000447713955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447713955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447713955 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 30, 30, 30, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000447713955 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 Building ZINC000447713955 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447713955 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 742) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl) `ZINC000447713955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447713955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447713955 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 30, 30, 30, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 743) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl) `ZINC000447713955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447713955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447713955 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1Cl 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 30, 30, 30, 19, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000447713955 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000447713955 Building ZINC000517668494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517668494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/744 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cc1) `ZINC000517668494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517668494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000517668494 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 6, 15, 15, 10, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 15, 15] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/745 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cc1) `ZINC000517668494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517668494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000517668494 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 15, 15, 9, 10, 15, 15, 15, 15, 15, 15, 15, 12, 12, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 15, 15, 15, 15] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517668494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 Building ZINC000517668494 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517668494 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 744) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cc1) `ZINC000517668494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517668494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000517668494 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 6, 15, 15, 10, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 15, 15] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 745) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cc1) `ZINC000517668494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517668494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000517668494 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 15, 15, 9, 10, 15, 15, 15, 15, 15, 15, 15, 12, 12, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 15, 15, 15, 15] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517668494 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517668494 Building ZINC000448515193 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000448515193 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/746 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(F)ccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000448515193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000448515193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000448515193 none Cc1c(F)ccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 9, 14, 14, 14, 14, 14, 4, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/747 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(F)ccc(Cl)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000448515193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000448515193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000448515193 none Cc1c(F)ccc(Cl)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 10, 14, 14, 14, 14, 14, 4, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000448515193 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 Building ZINC000448515193 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000448515193 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 746) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(F)ccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000448515193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000448515193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000448515193 none Cc1c(F)ccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 9, 14, 14, 14, 14, 14, 4, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 747) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(F)ccc(Cl)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000448515193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000448515193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000448515193 none Cc1c(F)ccc(Cl)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 22, 22, 22, 10, 14, 14, 14, 14, 14, 4, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000448515193 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000448515193 Building ZINC000517990412 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517990412 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/748 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517990412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990412 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 9, 9, 24, 25, 25, 24, 25, 25, 9, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 24, 24, 25, 25, 24, 25, 25, 9, 9, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/749 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517990412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990412 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 13, 13, 13, 13, 13, 13, 26, 27, 27, 26, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 26, 26, 27, 27, 27, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517990412 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 Building ZINC000517990412 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517990412 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 748) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517990412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990412 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 9, 9, 24, 25, 25, 24, 25, 25, 9, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 24, 24, 25, 25, 24, 25, 25, 9, 9, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 749) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517990412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990412 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 13, 13, 13, 13, 13, 13, 26, 27, 27, 26, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 26, 26, 27, 27, 27, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517990412 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990412 Building ZINC000517990413 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517990413 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/750 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517990413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990413 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 13, 13, 13, 13, 13, 13, 25, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 25, 27, 27, 27, 27, 27, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/751 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517990413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990413 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 11, 11, 11, 11, 11, 11, 25, 26, 26, 26, 26, 26, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 25, 25, 26, 26, 26, 26, 26, 11, 11, 5, 5, 5, 5, 5, 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]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517990413 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 Building ZINC000517990413 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517990413 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 750) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517990413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990413 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 13, 13, 13, 13, 13, 13, 25, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 25, 27, 27, 27, 27, 27, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 751) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000517990413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517990413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000517990413 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 6, 11, 11, 11, 11, 11, 11, 25, 26, 26, 26, 26, 26, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 25, 25, 26, 26, 26, 26, 26, 11, 11, 5, 5, 5, 5, 5, 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]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000517990413 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000517990413 Building ZINC000518311405 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518311405 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/752 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518311405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518311405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518311405 none Cc1ccc(F)c2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9] 35 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/753 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518311405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518311405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518311405 none Cc1ccc(F)c2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8] 35 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000518311405 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 Building ZINC000518311405 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518311405 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 752) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)c2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518311405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518311405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518311405 none Cc1ccc(F)c2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 3, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9] 35 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 753) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)c2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518311405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518311405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518311405 none Cc1ccc(F)c2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8] 35 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000518311405 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518311405 Building ZINC000518731240 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518731240 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/754 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000518731240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518731240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518731240 none Cc1ccc(F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/755 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000518731240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518731240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518731240 none Cc1ccc(F)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000518731240 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 Building ZINC000518731240 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518731240 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 754) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000518731240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518731240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518731240 none Cc1ccc(F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 755) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC000518731240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518731240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000518731240 none Cc1ccc(F)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 14 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000518731240 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000518731240 Building ZINC000521000649 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521000649 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/756 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000521000649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521000649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000521000649 none CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 28, 28, 28, 22, 22, 3, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/757 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000521000649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521000649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000521000649 none CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 22, 22, 2, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000521000649 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 Building ZINC000521000649 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521000649 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 756) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000521000649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521000649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000521000649 none CSCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 10, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 28, 28, 28, 22, 22, 3, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 757) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000521000649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521000649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000521000649 none CSCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 22, 22, 2, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000521000649 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000521000649 Building ZINC000452198552 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452198552 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/758 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452198552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198552 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 13, 13, 10, 13, 13, 25, 25, 13, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 13, 13, 10, 25, 25, 25, 25, 25, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/759 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452198552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198552 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 12, 12, 8, 12, 12, 26, 26, 12, 4, 4, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 8, 26, 26, 26, 26, 26, 12] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452198552 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 Building ZINC000452198552 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452198552 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 758) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452198552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198552 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 13, 13, 10, 13, 13, 25, 25, 13, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 13, 13, 10, 25, 25, 25, 25, 25, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 759) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452198552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198552 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 12, 12, 8, 12, 12, 26, 26, 12, 4, 4, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 8, 26, 26, 26, 26, 26, 12] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452198552 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198552 Building ZINC000452198555 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452198555 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/760 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452198555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198555 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 12, 12, 4, 12, 12, 27, 27, 12, 4, 4, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 4, 27, 27, 27, 27, 27, 12] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/761 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452198555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198555 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 5, 14, 14, 5, 14, 14, 25, 25, 14, 5, 5, 5, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 5, 25, 25, 25, 25, 25, 14] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452198555 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 Building ZINC000452198555 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452198555 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 760) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452198555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198555 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 4, 12, 12, 4, 12, 12, 27, 27, 12, 4, 4, 4, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 4, 27, 27, 27, 27, 27, 12] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 761) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1) `ZINC000452198555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452198555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000452198555 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccc(C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 5, 14, 14, 5, 14, 14, 25, 25, 14, 5, 5, 5, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 5, 25, 25, 25, 25, 25, 14] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452198555 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452198555 Building ZINC000452269053 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452269053 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/762 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1) `ZINC000452269053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452269053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269053 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/763 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1) `ZINC000452269053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452269053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269053 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 25, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 4, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452269053 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 Building ZINC000452269053 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452269053 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 762) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1) `ZINC000452269053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452269053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269053 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 763) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1) `ZINC000452269053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452269053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269053 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(C)nc1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 25, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 4, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452269053 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269053 Building ZINC000452269725 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452269725 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/764 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1) `ZINC000452269725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452269725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269725 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/765 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1) `ZINC000452269725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452269725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269725 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452269725 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 Building ZINC000452269725 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452269725 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 764) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1) `ZINC000452269725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452269725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269725 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 765) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1) `ZINC000452269725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452269725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000452269725 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)nc2C2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 8, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452269725 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452269725 Building ZINC000452305153 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452305153 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/766 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)CCCC2=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000452305153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452305153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452305153 none O=C(Nc1ccc2c(c1)CCCC2=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 24, 24, 24, 22, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/767 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)CCCC2=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000452305153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452305153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452305153 none O=C(Nc1ccc2c(c1)CCCC2=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 23, 23, 23, 20, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452305153 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 Building ZINC000452305153 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452305153 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 766) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc2c(c1)CCCC2=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000452305153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452305153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452305153 none O=C(Nc1ccc2c(c1)CCCC2=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 24, 24, 24, 22, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 767) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccc2c(c1)CCCC2=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000452305153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452305153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452305153 none O=C(Nc1ccc2c(c1)CCCC2=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 23, 23, 23, 20, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452305153 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452305153 Building ZINC000522736374 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522736374 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/768 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1) `ZINC000522736374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522736374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000522736374 none CCCc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 20, 18, 24, 24, 14, 10, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 24, 24, 39, 39, 39, 39, 39, 24, 24, 24, 24, 14, 14, 3, 8, 8, 8, 8, 8, 14, 14, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/769 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1) `ZINC000522736374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522736374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000522736374 none CCCc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 6, 24, 24, 4, 3, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 23, 24, 37, 37, 37, 37, 37, 24, 24, 24, 24, 14, 14, 3, 8, 8, 8, 8, 8, 14, 14, 23, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000522736374 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 Building ZINC000522736374 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522736374 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 768) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1) `ZINC000522736374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522736374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000522736374 none CCCc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 20, 18, 24, 24, 14, 10, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 24, 24, 39, 39, 39, 39, 39, 24, 24, 24, 24, 14, 14, 3, 8, 8, 8, 8, 8, 14, 14, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 769) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1) `ZINC000522736374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522736374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000522736374 none CCCc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 6, 24, 24, 4, 3, 14, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 23, 24, 37, 37, 37, 37, 37, 24, 24, 24, 24, 14, 14, 3, 8, 8, 8, 8, 8, 14, 14, 23, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000522736374 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522736374 Building ZINC000522942020 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522942020 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/770 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1) `ZINC000522942020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522942020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000522942020 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/771 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1) `ZINC000522942020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522942020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000522942020 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000522942020 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 Building ZINC000522942020 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522942020 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 770) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1) `ZINC000522942020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522942020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000522942020 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 771) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1) `ZINC000522942020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522942020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000522942020 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(F)c1 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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000522942020 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000522942020 Building ZINC000452686111 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452686111 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/772 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1) `ZINC000452686111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452686111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452686111 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 14, 14, 4, 14, 14, 14, 20, 20, 20, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 14, 14, 4, 14, 20, 20, 20, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/773 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1) `ZINC000452686111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452686111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452686111 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 5, 12, 12, 12, 19, 19, 19, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 12, 12, 5, 12, 19, 19, 19, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452686111 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 Building ZINC000452686111 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452686111 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 772) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1) `ZINC000452686111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452686111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452686111 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 4, 4, 14, 14, 4, 14, 14, 14, 20, 20, 20, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 14, 14, 4, 14, 20, 20, 20, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 773) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1) `ZINC000452686111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452686111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452686111 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(C)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 5, 12, 12, 12, 19, 19, 19, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 4, 12, 12, 5, 12, 19, 19, 19, 8] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452686111 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452686111 Building ZINC000452845958 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452845958 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/774 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2ccccc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000452845958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452845958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000452845958 none Cc1cc2ccccc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 17] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/775 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2ccccc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000452845958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452845958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000452845958 none Cc1cc2ccccc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452845958 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 Building ZINC000452845958 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452845958 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 774) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc2ccccc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000452845958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452845958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000452845958 none Cc1cc2ccccc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 17] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 775) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc2ccccc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000452845958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452845958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000452845958 none Cc1cc2ccccc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452845958 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452845958 Building ZINC000452855336 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452855336 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/776 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000452855336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452855336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452855336 none Cc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 10, 15, 15, 15, 15, 15, 15, 15, 5, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/777 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000452855336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452855336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452855336 none Cc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 11, 13, 13, 13, 13, 13, 13, 13, 4, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452855336 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 Building ZINC000452855336 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452855336 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 776) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000452855336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452855336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452855336 none Cc1cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 10, 15, 15, 15, 15, 15, 15, 15, 5, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 777) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000452855336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452855336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000452855336 none Cc1cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 11, 13, 13, 13, 13, 13, 13, 13, 4, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000452855336 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000452855336 Building ZINC000523857419 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523857419 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/778 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)c2c1cccc2F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000523857419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523857419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000523857419 none O=C(N1CC2(CCC2)c2c1cccc2F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/779 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCC2)c2c1cccc2F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000523857419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523857419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000523857419 none O=C(N1CC2(CCC2)c2c1cccc2F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000523857419 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 Building ZINC000523857419 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523857419 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 778) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC2(CCC2)c2c1cccc2F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000523857419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523857419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000523857419 none O=C(N1CC2(CCC2)c2c1cccc2F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 779) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC2(CCC2)c2c1cccc2F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000523857419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523857419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000523857419 none O=C(N1CC2(CCC2)c2c1cccc2F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9] 31 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000523857419 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000523857419 Building ZINC000524487547 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524487547 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/780 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12) `ZINC000524487547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524487547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000524487547 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/781 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12) `ZINC000524487547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524487547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000524487547 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000524487547 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 Building ZINC000524487547 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524487547 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 780) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12) `ZINC000524487547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524487547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000524487547 none Cc1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 781) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12) `ZINC000524487547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524487547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000524487547 none Cc1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)oc2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.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', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000524487547 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524487547 Building ZINC000524851234 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524851234 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/782 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000524851234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524851234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000524851234 none O=C(Nc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 15, 21, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 21, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/783 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000524851234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524851234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000524851234 none O=C(Nc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 16, 24, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 24, 24, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000524851234 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 Building ZINC000524851234 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524851234 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 782) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000524851234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524851234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000524851234 none O=C(Nc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 15, 21, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 21, 21, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 783) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000524851234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524851234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000524851234 none O=C(Nc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 5, 7, 7, 7, 16, 24, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 24, 24, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000524851234 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000524851234 Building ZINC000526957846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000526957846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/784 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cs1) `ZINC000526957846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000526957846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000526957846 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 17, 37, 37, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 37, 37, 50, 50, 50, 50, 50, 37, 37, 12, 12, 2, 2, 2, 1, 2, 2, 37, 37, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/785 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cs1) `ZINC000526957846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000526957846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000526957846 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 18, 36, 36, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 36, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 2, 2, 1, 2, 2, 36, 36, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000526957846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 Building ZINC000526957846 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000526957846 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 784) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cs1) `ZINC000526957846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000526957846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000526957846 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 17, 37, 37, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 37, 37, 50, 50, 50, 50, 50, 37, 37, 12, 12, 2, 2, 2, 1, 2, 2, 37, 37, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 785) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cs1) `ZINC000526957846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000526957846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000526957846 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 18, 36, 36, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 36, 36, 50, 50, 50, 50, 50, 36, 36, 11, 11, 2, 2, 2, 1, 2, 2, 36, 36, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000526957846 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000526957846 Building ZINC000527193480 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527193480 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/786 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)s2)cs1) `ZINC000527193480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527193480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000527193480 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 39, 50, 50, 50, 50, 50, 39, 39, 11, 11, 2, 2, 2, 1, 2, 2, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/787 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)s2)cs1) `ZINC000527193480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527193480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000527193480 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 39, 50, 50, 50, 50, 50, 39, 39, 11, 11, 2, 2, 2, 1, 2, 2, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000527193480 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 Building ZINC000527193480 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527193480 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 786) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)s2)cs1) `ZINC000527193480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527193480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000527193480 none Cc1nc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 39, 50, 50, 50, 50, 50, 39, 39, 11, 11, 2, 2, 2, 1, 2, 2, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 787) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)s2)cs1) `ZINC000527193480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527193480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000527193480 none Cc1nc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 39, 39, 39, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 39, 50, 50, 50, 50, 50, 39, 39, 11, 11, 2, 2, 2, 1, 2, 2, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000527193480 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000527193480 Building ZINC000456038981 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456038981 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/788 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000456038981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456038981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000456038981 none CCOc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 7, 8, 22, 22, 22, 22, 22, 8, 8, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/789 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000456038981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456038981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000456038981 none CCOc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 7, 9, 27, 27, 27, 27, 27, 9, 9, 4, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000456038981 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 Building ZINC000456038981 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456038981 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 788) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000456038981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456038981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000456038981 none CCOc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 7, 8, 22, 22, 22, 22, 22, 8, 8, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 789) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCOc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000456038981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456038981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000456038981 none CCOc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 7, 9, 27, 27, 27, 27, 27, 9, 9, 4, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000456038981 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456038981 Building ZINC000456480584 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456480584 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/790 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000456480584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456480584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000456480584 none CCSCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 14, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 14, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 37, 37, 37, 37, 37, 14, 14, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/791 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000456480584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456480584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000456480584 none CCSCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 14, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 37, 37, 37, 37, 37, 14, 14, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000456480584 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 Building ZINC000456480584 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456480584 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 790) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCSCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000456480584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456480584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000456480584 none CCSCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 14, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 14, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 37, 37, 37, 37, 37, 14, 14, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 791) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCSCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000456480584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456480584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000456480584 none CCSCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', '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.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 14, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 37, 37, 37, 37, 37, 14, 14, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000456480584 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000456480584 Building ZINC000457902508 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457902508 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/792 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC) `ZINC000457902508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457902508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000457902508 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 22, 20, 20, 20, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/793 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC) `ZINC000457902508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457902508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000457902508 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 21, 20, 20, 20, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000457902508 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 Building ZINC000457902508 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457902508 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 792) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC) `ZINC000457902508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457902508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000457902508 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 22, 20, 20, 20, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 793) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC) `ZINC000457902508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457902508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000457902508 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 21, 20, 20, 20, 10, 10, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000457902508 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000457902508 Building ZINC000458204166 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458204166 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/794 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458204166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204166 none CC(C)[C@@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 17, 17, 9, 1, 9, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/795 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458204166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204166 none CC(C)[C@@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 17, 17, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 17, 17, 17, 17, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458204166 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 Building ZINC000458204166 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458204166 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 794) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458204166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204166 none CC(C)[C@@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 17, 17, 9, 1, 9, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 795) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458204166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204166 none CC(C)[C@@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 17, 17, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 17, 17, 17, 17, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458204166 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204166 Building ZINC000458204168 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458204168 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/796 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458204168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204168 none CC(C)[C@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 19, 19, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 19, 19, 19, 19, 19, 19, 19, 25, 25, 25, 25, 25, 25, 25, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 112 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/797 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458204168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204168 none CC(C)[C@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 23, 18, 18, 7, 1, 8, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 23, 23, 23, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458204168 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 Building ZINC000458204168 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458204168 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 796) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458204168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204168 none CC(C)[C@H]1N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 19, 19, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 19, 19, 19, 19, 19, 19, 19, 25, 25, 25, 25, 25, 25, 25, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 112 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 797) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2) `ZINC000458204168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458204168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000458204168 none CC(C)[C@H]1N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 23, 18, 18, 7, 1, 8, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 23, 23, 23, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458204168 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458204168 Building ZINC000458284852 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458284852 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/798 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458284852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284852 none C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 27, 27, 27, 27, 27, 27, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 17, 17, 27, 27, 27, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/799 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458284852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284852 none C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 18, 29, 29, 29, 29, 29, 29, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 29, 29, 29, 29, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458284852 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 Building ZINC000458284852 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458284852 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 798) grep: /scratch/xiaobo/132203/xbs-8058115.45/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[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458284852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284852 none C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 27, 27, 27, 27, 27, 27, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 17, 17, 27, 27, 27, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 799) grep: /scratch/xiaobo/132203/xbs-8058115.45/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[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458284852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284852 none C[C@@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 18, 29, 29, 29, 29, 29, 29, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 29, 29, 29, 29, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458284852 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284852 Building ZINC000458284854 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458284854 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/800 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458284854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284854 none C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 18, 29, 29, 29, 29, 29, 29, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 18, 18, 29, 29, 29, 29, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/801 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458284854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284854 none C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 18, 18, 27, 27, 27, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458284854 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 Building ZINC000458284854 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458284854 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 800) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458284854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284854 none C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 10, 10, 18, 29, 29, 29, 29, 29, 29, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 18, 18, 29, 29, 29, 29, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 801) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000458284854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458284854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000458284854 none C[C@H](Cc1cccc(F)c1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 2, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 18, 18, 27, 27, 27, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000458284854 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000458284854 Building ZINC000460621742 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000460621742 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/802 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000460621742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621742 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 18, 18, 18, 15, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 24, 24, 24, 24, 24, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/803 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000460621742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621742 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 19, 15, 3, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000460621742 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 Building ZINC000460621742 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000460621742 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 802) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000460621742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621742 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 18, 18, 18, 15, 3, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 24, 24, 24, 24, 24, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 803) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000460621742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621742 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 19, 19, 15, 3, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000460621742 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621742 Building ZINC000460621743 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000460621743 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/804 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000460621743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621743 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 15, 3, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/805 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000460621743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621743 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 13, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000460621743 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 Building ZINC000460621743 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000460621743 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 804) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000460621743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621743 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 21, 21, 15, 3, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 28, 28, 28, 28, 28, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 805) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1) `ZINC000460621743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000460621743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000460621743 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 18, 18, 13, 3, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000460621743 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000460621743 Building ZINC000464100274 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464100274 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/806 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000464100274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464100274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000464100274 none CC(C)(C)c1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 29, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/807 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000464100274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464100274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000464100274 none CC(C)(C)c1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 28, 28, 14, 14, 14, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000464100274 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 Building ZINC000464100274 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464100274 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 806) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)c1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000464100274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464100274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000464100274 none CC(C)(C)c1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 29, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 807) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)c1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000464100274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464100274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000464100274 none CC(C)(C)c1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 28, 28, 14, 14, 14, 7, 7, 1, 7, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000464100274 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000464100274 Building ZINC000534321990 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534321990 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/808 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12) `ZINC000534321990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534321990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534321990 none COc1ccnc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 25, 25, 25, 20, 20, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/809 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12) `ZINC000534321990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534321990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534321990 none COc1ccnc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 27, 27, 27, 21, 21, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000534321990 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 Building ZINC000534321990 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000534321990 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 808) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccnc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12) `ZINC000534321990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000534321990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534321990 none COc1ccnc2c(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 25, 25, 25, 20, 20, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 809) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccnc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12) `ZINC000534321990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000534321990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000534321990 none COc1ccnc2c(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 27, 27, 27, 21, 21, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000534321990 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000534321990 Building ZINC000537148918 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000537148918 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/810 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000537148918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000537148918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000537148918 none CC(C)(C)CN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 6, 5, 6, 7, 10, 10, 10, 1, 5, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/811 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000537148918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000537148918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000537148918 none CC(C)(C)CN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 2, 3, 5, 5, 5, 1, 2, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 21 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000537148918 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 Building ZINC000537148918 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000537148918 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 810) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000537148918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000537148918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000537148918 none CC(C)(C)CN(CC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 6, 5, 6, 7, 10, 10, 10, 1, 5, 1, 1, 1, 12, 12, 12, 12, 25, 25, 25, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 811) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000537148918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000537148918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000537148918 none CC(C)(C)CN(CC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 8, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 2, 3, 5, 5, 5, 1, 2, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 21 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000537148918 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000537148918 Building ZINC000539536579 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539536579 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/812 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1) `ZINC000539536579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539536579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000539536579 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 19, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/813 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1) `ZINC000539536579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539536579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000539536579 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 25, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000539536579 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 Building ZINC000539536579 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539536579 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 812) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1) `ZINC000539536579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539536579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000539536579 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 19, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 813) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1) `ZINC000539536579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539536579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000539536579 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 25, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000539536579 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539536579 Building ZINC000469696411 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469696411 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/814 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000469696411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469696411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000469696411 none CC(C)Nc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 27, 8, 8, 8, 6, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 22, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/815 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000469696411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469696411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000469696411 none CC(C)Nc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 23, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000469696411 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 Building ZINC000469696411 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469696411 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 814) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000469696411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469696411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000469696411 none CC(C)Nc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 27, 8, 8, 8, 6, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 22, 8, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 815) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000469696411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469696411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000469696411 none CC(C)Nc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 6, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 23, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000469696411 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000469696411 Building ZINC000539993366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539993366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/816 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C2=CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1) `ZINC000539993366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539993366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000539993366 none Cc1cccc(C2=CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 30, 30, 30, 30, 9, 30, 30, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 30] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/817 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C2=CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1) `ZINC000539993366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539993366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000539993366 none Cc1cccc(C2=CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 29, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 29, 29, 29, 29, 28, 29, 29, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 29] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000539993366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 Building ZINC000539993366 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000539993366 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 816) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc(C2=CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1) `ZINC000539993366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000539993366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000539993366 none Cc1cccc(C2=CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 30, 30, 30, 30, 9, 30, 30, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 30] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 817) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc(C2=CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1) `ZINC000539993366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000539993366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000539993366 none Cc1cccc(C2=CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 29, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 29, 29, 29, 29, 28, 29, 29, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 29] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000539993366 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000539993366 Building ZINC000470072587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470072587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/818 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000470072587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470072587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470072587 none CC(C)Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 8, 8, 8, 5, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 20, 8, 5, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/819 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000470072587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470072587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470072587 none CC(C)Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 26, 8, 8, 8, 5, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 21, 8, 5, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470072587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 Building ZINC000470072587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470072587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 818) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000470072587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470072587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470072587 none CC(C)Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 8, 8, 8, 5, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 20, 8, 5, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 819) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000470072587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470072587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470072587 none CC(C)Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 26, 8, 8, 8, 5, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 21, 8, 5, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470072587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470072587 Building ZINC000470194474 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194474 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/820 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194474 none CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 26, 31, 26, 26, 26, 26, 26, 6, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 26, 26, 31, 31, 31, 31, 31, 31, 31, 26, 26, 26, 26, 26, 26, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/821 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194474 none CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 27, 24, 24, 24, 24, 24, 7, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 24, 24, 27, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 24, 24, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 24, 24, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194474 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 Building ZINC000470194474 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194474 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 820) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194474 none CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 26, 31, 26, 26, 26, 26, 26, 6, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 26, 26, 31, 31, 31, 31, 31, 31, 31, 26, 26, 26, 26, 26, 26, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 821) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194474 none CC(C)[C@@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 27, 24, 24, 24, 24, 24, 7, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 24, 24, 27, 27, 27, 27, 27, 27, 27, 24, 24, 24, 24, 24, 24, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 24, 24, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194474 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194474 Building ZINC000470194476 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194476 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/822 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194476 none CC(C)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 33, 25, 25, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 25, 25, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/823 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194476 none CC(C)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 32, 26, 26, 26, 26, 26, 7, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 26, 26, 32, 32, 32, 32, 32, 32, 32, 26, 26, 26, 26, 26, 26, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194476 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 Building ZINC000470194476 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194476 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 822) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194476 none CC(C)[C@H]1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 33, 25, 25, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 25, 25, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 823) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194476 none CC(C)[C@H]1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 32, 26, 26, 26, 26, 26, 7, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 26, 26, 32, 32, 32, 32, 32, 32, 32, 26, 26, 26, 26, 26, 26, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194476 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194476 Building ZINC000470194477 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194477 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/824 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194477 none CC(C)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 33, 25, 25, 25, 25, 25, 4, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 25, 25, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/825 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194477 none CC(C)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 32, 27, 27, 27, 27, 27, 4, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27, 27, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194477 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 Building ZINC000470194477 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194477 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 824) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194477 none CC(C)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 33, 25, 25, 25, 25, 25, 4, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 25, 25, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 825) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194477 none CC(C)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 32, 27, 27, 27, 27, 27, 4, 24, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27, 27, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194477 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194477 Building ZINC000470194478 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194478 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/826 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194478 none CC(C)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 36, 28, 28, 28, 28, 28, 5, 28, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 28, 28, 36, 36, 36, 36, 36, 36, 36, 28, 28, 28, 28, 28, 28, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/827 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194478 none CC(C)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 37, 30, 30, 30, 30, 30, 6, 30, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 30, 30, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30, 30, 30, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194478 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 Building ZINC000470194478 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470194478 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 826) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470194478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194478 none CC(C)[C@@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 36, 28, 28, 28, 28, 28, 5, 28, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 28, 28, 36, 36, 36, 36, 36, 36, 36, 28, 28, 28, 28, 28, 28, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 827) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000470194478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470194478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470194478 none CC(C)[C@@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 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, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 37, 30, 30, 30, 30, 30, 6, 30, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 30, 30, 37, 37, 37, 37, 37, 37, 37, 30, 30, 30, 30, 30, 30, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000470194478 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000470194478 Building ZINC000471749817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471749817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/828 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000471749817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471749817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000471749817 none O=C(NCc1ccc(COc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 12, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/829 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000471749817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471749817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000471749817 none O=C(NCc1ccc(COc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 15, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000471749817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 Building ZINC000471749817 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471749817 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 828) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCc1ccc(COc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000471749817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471749817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000471749817 none O=C(NCc1ccc(COc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 12, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 829) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(NCc1ccc(COc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000471749817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471749817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000471749817 none O=C(NCc1ccc(COc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 15, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 9, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000471749817 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000471749817 Building ZINC000472215386 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472215386 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/830 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000472215386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472215386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000472215386 none CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 17, 34, 5, 17, 17, 35, 42, 42, 35, 35, 42, 42, 3, 5, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 34, 34, 34, 34, 34, 34, 34, 35, 35, 42, 42, 42, 42, 5, 5, 5, 4, 4, 1, 4, 4] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/831 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000472215386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472215386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000472215386 none CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 27, 5, 15, 15, 31, 41, 41, 41, 41, 41, 41, 3, 5, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 27, 27, 31, 31, 41, 41, 41, 41, 5, 5, 5, 4, 4, 1, 4, 4] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000472215386 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 Building ZINC000472215386 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472215386 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 830) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000472215386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472215386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000472215386 none CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 17, 34, 5, 17, 17, 35, 42, 42, 35, 35, 42, 42, 3, 5, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 34, 34, 34, 34, 34, 34, 34, 35, 35, 42, 42, 42, 42, 5, 5, 5, 4, 4, 1, 4, 4] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 263 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 831) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000472215386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472215386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000472215386 none CC(C)[C@H](Cc1ccc(F)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 15, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 27, 5, 15, 15, 31, 41, 41, 41, 41, 41, 41, 3, 5, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 27, 27, 27, 27, 27, 27, 27, 31, 31, 41, 41, 41, 41, 5, 5, 5, 4, 4, 1, 4, 4] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000472215386 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000472215386 Building ZINC000543232554 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543232554 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/832 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543232554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232554 none Cc1cccc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 29, 10, 10, 10, 10, 10, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 29, 29, 29, 29, 10, 29, 29, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/833 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543232554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232554 none Cc1cccc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 9, 30, 30, 30, 30, 9, 30, 30, 9, 9, 9, 9, 4, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000543232554 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 Building ZINC000543232554 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543232554 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 832) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543232554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232554 none Cc1cccc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 29, 10, 10, 10, 10, 10, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 29, 29, 29, 29, 10, 29, 29, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 833) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543232554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232554 none Cc1cccc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 9, 30, 30, 30, 30, 9, 30, 30, 9, 9, 9, 9, 4, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000543232554 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232554 Building ZINC000543232558 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543232558 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/834 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543232558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232558 none Cc1cccc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 28, 28, 9, 9, 9, 9, 9, 2, 1, 5, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 9, 28, 28, 28, 28, 26, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/835 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543232558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232558 none Cc1cccc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 31, 10, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 31, 31, 31, 31, 21, 31, 31, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000543232558 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 Building ZINC000543232558 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543232558 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 834) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543232558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232558 none Cc1cccc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 28, 28, 9, 9, 9, 9, 9, 2, 1, 5, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 9, 28, 28, 28, 28, 26, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 835) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000543232558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543232558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000543232558 none Cc1cccc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 31, 10, 10, 10, 10, 10, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 31, 31, 31, 31, 21, 31, 31, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000543232558 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000543232558 Building ZINC000545314120 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545314120 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/836 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12) `ZINC000545314120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545314120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC000545314120 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 26, 26, 26, 21, 21, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/837 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12) `ZINC000545314120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545314120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC000545314120 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545314120 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 Building ZINC000545314120 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545314120 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 836) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12) `ZINC000545314120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545314120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC000545314120 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 26, 26, 26, 21, 21, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 837) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12) `ZINC000545314120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545314120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC000545314120 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545314120 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545314120 Building ZINC000545446214 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545446214 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/838 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl) `ZINC000545446214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545446214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545446214 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 13, 15, 15, 14, 15, 15, 5, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 13, 13, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/839 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl) `ZINC000545446214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545446214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545446214 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 15, 17, 17, 16, 17, 17, 6, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545446214 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 Building ZINC000545446214 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545446214 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 838) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl) `ZINC000545446214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545446214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545446214 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 13, 15, 15, 14, 15, 15, 5, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 13, 13, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 839) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl) `ZINC000545446214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545446214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545446214 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 15, 17, 17, 16, 17, 17, 6, 7, 7, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545446214 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545446214 Building ZINC000545480921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/840 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480921 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 23, 23, 21, 22, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 12, 12, 21, 21, 21, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/841 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480921 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545480921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 Building ZINC000545480921 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480921 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 840) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480921 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 23, 23, 21, 22, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 12, 12, 21, 21, 21, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 841) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480921 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545480921 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480921 Building ZINC000545480923 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480923 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/842 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480923 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/843 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480923 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 23, 23, 21, 21, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 12, 12, 21, 21, 21, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545480923 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 Building ZINC000545480923 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480923 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 842) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480923 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 843) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl) `ZINC000545480923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545480923 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)c2ccc(C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 23, 23, 21, 21, 23, 23, 6, 6, 6, 12, 12, 12, 6, 6, 2, 12, 12, 21, 21, 21, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000545480923 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000545480923 Building ZINC000546190321 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546190321 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/844 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(Cc1ccccc1F)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000546190321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546190321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546190321 none CCCCN(Cc1ccccc1F)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 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: [25, 20, 17, 7, 3, 7, 17, 24, 24, 20, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 25, 25, 25, 25, 25, 21, 21, 17, 17, 17, 17, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/845 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(Cc1ccccc1F)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000546190321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546190321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546190321 none CCCCN(Cc1ccccc1F)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 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: [25, 20, 17, 7, 3, 7, 17, 25, 25, 25, 25, 25, 25, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 25, 25, 25, 25, 25, 21, 21, 17, 17, 17, 17, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000546190321 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 Building ZINC000546190321 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546190321 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 844) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCN(Cc1ccccc1F)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000546190321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546190321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546190321 none CCCCN(Cc1ccccc1F)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 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: [25, 20, 17, 7, 3, 7, 17, 24, 24, 20, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 25, 25, 25, 25, 25, 21, 21, 17, 17, 17, 17, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 845) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCN(Cc1ccccc1F)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000546190321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546190321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546190321 none CCCCN(Cc1ccccc1F)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 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: [25, 20, 17, 7, 3, 7, 17, 25, 25, 25, 25, 25, 25, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 25, 25, 25, 25, 25, 21, 21, 17, 17, 17, 17, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000546190321 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000546190321 Building ZINC000600605759 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000600605759 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/846 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2(CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000600605759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000600605759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000600605759 none O=C(N1CCCC2(CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/847 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2(CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000600605759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000600605759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000600605759 none O=C(N1CCCC2(CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000600605759 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 Building ZINC000600605759 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000600605759 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 846) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCCC2(CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000600605759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000600605759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000600605759 none O=C(N1CCCC2(CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 847) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CCCC2(CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000600605759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000600605759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000600605759 none O=C(N1CCCC2(CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/132203/xbs-8058115.45/working/building/ZINC000600605759 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000600605759 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000600605759 Building ZINC000478193622 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478193622 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/848 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478193622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193622 none O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 25, 25, 22, 24, 25, 25, 17, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 17, 25, 25, 25, 25, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/849 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478193622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193622 none O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 20, 20, 20, 20, 28, 28, 21, 21, 28, 28, 20, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 28, 28, 28, 28, 20, 20, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000478193622 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 Building ZINC000478193622 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478193622 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 848) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478193622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193622 none O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 25, 25, 22, 24, 25, 25, 17, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 17, 17, 17, 17, 25, 25, 25, 25, 17, 17, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 849) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478193622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193622 none O=C(N1CC[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 20, 20, 20, 20, 28, 28, 21, 21, 28, 28, 20, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 28, 28, 28, 28, 20, 20, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000478193622 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193622 Building ZINC000478193624 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478193624 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/850 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478193624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193624 none O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 20, 20, 20, 20, 20, 27, 27, 20, 20, 27, 27, 20, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 27, 27, 27, 27, 20, 20, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/851 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478193624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193624 none O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 18, 18, 18, 18, 18, 24, 24, 19, 19, 24, 24, 18, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 24, 24, 24, 24, 18, 18, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000478193624 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 Building ZINC000478193624 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478193624 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 850) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478193624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193624 none O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 20, 20, 20, 20, 20, 27, 27, 20, 20, 27, 27, 20, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 27, 27, 27, 27, 20, 20, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 851) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000478193624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478193624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000478193624 none O=C(N1CC[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 7, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 6, 18, 18, 18, 18, 18, 24, 24, 19, 19, 24, 24, 18, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 24, 24, 24, 24, 18, 18, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000478193624 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000478193624 Building ZINC000481723612 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481723612 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/852 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000481723612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481723612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000481723612 none O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 14, 15, 15, 15, 15, 23, 23, 15, 15, 23, 23, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 23, 23, 23, 23, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/853 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000481723612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481723612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000481723612 none O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 15, 16, 16, 16, 16, 23, 23, 16, 23, 23, 23, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 23, 23, 23, 23, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000481723612 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 Building ZINC000481723612 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000481723612 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 852) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000481723612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000481723612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000481723612 none O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 14, 15, 15, 15, 15, 23, 23, 15, 15, 23, 23, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 15, 15, 23, 23, 23, 23, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 853) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000481723612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000481723612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000481723612 none O=C(N[C@H]1C[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 15, 16, 16, 16, 16, 23, 23, 16, 23, 23, 23, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 16, 16, 23, 23, 23, 23, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000481723612 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000481723612 Building ZINC000677286630 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000677286630 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/854 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000677286630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000677286630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000677286630 none O=C(Nc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 11, 11, 11, 11, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/855 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000677286630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000677286630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000677286630 none O=C(Nc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 13, 13, 13, 13, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000677286630 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 Building ZINC000677286630 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000677286630 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 854) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000677286630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000677286630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000677286630 none O=C(Nc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 11, 11, 11, 11, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 855) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000677286630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000677286630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000677286630 none O=C(Nc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 13, 13, 13, 13, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000677286630 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000677286630 Building ZINC000679526167 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526167 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/856 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526167 none C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8] 36 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/857 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526167 none C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 14, 1, 1, 1, 10, 10, 15, 15, 10, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 15, 15, 15, 15, 15, 15, 15, 15] 37 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526167 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 Building ZINC000679526167 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526167 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 856) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526167 none C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8] 36 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 857) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526167 none C[C@@H]1CC[C@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 14, 1, 1, 1, 10, 10, 15, 15, 10, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 15, 15, 15, 15, 15, 15, 15, 15] 37 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526167 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526167 Building ZINC000679526179 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526179 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/858 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526179 none C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 17, 2, 17, 1, 1, 1, 9, 9, 12, 12, 9, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/859 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526179 none C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 2, 16, 1, 1, 1, 10, 10, 17, 17, 10, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 17, 17, 17, 17, 17, 17, 17, 17] 49 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526179 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 Building ZINC000679526179 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679526179 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 858) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679526179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526179 none C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 17, 2, 17, 1, 1, 1, 9, 9, 12, 12, 9, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 12, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 859) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000679526179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679526179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000679526179 none C[C@H]1CC[C@@H](C(F)(F)F)CN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 15, 15, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 2, 16, 1, 1, 1, 10, 10, 17, 17, 10, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 17, 17, 17, 17, 17, 17, 17, 17] 49 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000679526179 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000679526179 Building ZINC000683245376 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000683245376 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/860 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000683245376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000683245376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683245376 none Cc1cccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 31, 35, 35, 22, 9, 9, 9, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 9, 35, 35, 35, 35, 35, 35, 35, 22, 22, 9, 9, 9, 2, 2, 9, 9, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/861 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000683245376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000683245376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683245376 none Cc1cccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 36, 37, 37, 23, 10, 10, 10, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 37, 37, 37, 37, 37, 37, 37, 23, 23, 10, 10, 10, 3, 3, 10, 10, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000683245376 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 Building ZINC000683245376 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000683245376 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 860) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000683245376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000683245376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683245376 none Cc1cccc(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 31, 35, 35, 22, 9, 9, 9, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 9, 35, 35, 35, 35, 35, 35, 35, 22, 22, 9, 9, 9, 2, 2, 9, 9, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 861) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000683245376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000683245376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683245376 none Cc1cccc(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 36, 37, 37, 23, 10, 10, 10, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 37, 37, 37, 37, 37, 37, 37, 23, 23, 10, 10, 10, 3, 3, 10, 10, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000683245376 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683245376 Building ZINC000683247504 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000683247504 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/862 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000683247504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000683247504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683247504 none Cc1ccccc1CC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 25, 35, 35, 25, 9, 9, 9, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 9, 35, 35, 35, 35, 30, 35, 35, 25, 25, 9, 9, 9, 3, 3, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/863 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000683247504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000683247504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683247504 none Cc1ccccc1CC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 27, 39, 39, 27, 9, 9, 9, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 39, 39, 39, 39, 27, 39, 39, 27, 27, 9, 9, 9, 4, 4, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000683247504 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 Building ZINC000683247504 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000683247504 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 862) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1CC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000683247504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000683247504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683247504 none Cc1ccccc1CC1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 25, 35, 35, 25, 9, 9, 9, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 9, 35, 35, 35, 35, 30, 35, 35, 25, 25, 9, 9, 9, 3, 3, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 863) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccccc1CC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000683247504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000683247504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000683247504 none Cc1ccccc1CC1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 27, 39, 39, 27, 9, 9, 9, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 39, 39, 39, 39, 27, 39, 39, 27, 27, 9, 9, 9, 4, 4, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000683247504 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000683247504 Building ZINC000684780737 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000684780737 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/864 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCc2sccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000684780737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000684780737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000684780737 none O=C(N1CCCCc2sccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 14, 1, 1, 1, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 23, 27, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/865 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCCc2sccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000684780737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000684780737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000684780737 none O=C(N1CCCCc2sccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 14, 1, 1, 1, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 25, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10, 10, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000684780737 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 Building ZINC000684780737 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000684780737 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 864) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(N1CCCCc2sccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000684780737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000684780737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000684780737 none O=C(N1CCCCc2sccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 14, 1, 1, 1, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 23, 27, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 865) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(N1CCCCc2sccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000684780737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000684780737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000684780737 none O=C(N1CCCCc2sccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 14, 1, 1, 1, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 21, 25, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10, 10, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000684780737 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000684780737 Building ZINC000864066557 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000864066557 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/866 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COC(C)(C)CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000864066557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000864066557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000864066557 none CC[C@@H]1COC(C)(C)CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 2, 15, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 36, 36, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 2, 5] 44 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]) total number of confs: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/867 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COC(C)(C)CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000864066557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000864066557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000864066557 none CC[C@@H]1COC(C)(C)CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 2, 14, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 33, 33, 33, 33, 33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 5] 38 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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000864066557 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 Building ZINC000864066557 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000864066557 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 866) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1COC(C)(C)CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000864066557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000864066557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000864066557 none CC[C@@H]1COC(C)(C)CN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 2, 15, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 36, 36, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 2, 5] 44 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]) total number of confs: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 867) grep: /scratch/xiaobo/132203/xbs-8058115.45/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@@H]1COC(C)(C)CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC000864066557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000864066557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000864066557 none CC[C@@H]1COC(C)(C)CN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 2, 14, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 33, 33, 33, 33, 33, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 5] 38 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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000864066557 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000864066557 Building ZINC000911205930 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911205930 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/868 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1) `ZINC000911205930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911205930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911205930 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 12, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/869 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1) `ZINC000911205930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911205930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911205930 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911205930 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 Building ZINC000911205930 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911205930 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 868) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1) `ZINC000911205930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911205930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911205930 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 2, 12, 18, 18, 18, 18, 18, 18, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 18, 18, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 869) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1) `ZINC000911205930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911205930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911205930 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccnc(Cl)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 16, 8, 1, 1, 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, 4, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 1, 1, 12, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 17, 17, 2, 2] 50 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911205930 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911205930 Building ZINC000911261155 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911261155 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/870 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1) `ZINC000911261155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911261155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000911261155 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 15, 17, 17, 17, 18, 17, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 17, 17, 18, 18, 18, 18, 18, 18, 6, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/871 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1) `ZINC000911261155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911261155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000911261155 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 15, 18, 19, 19, 19, 19, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911261155 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 Building ZINC000911261155 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911261155 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 870) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1) `ZINC000911261155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911261155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000911261155 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 5, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 15, 17, 17, 17, 18, 17, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 17, 17, 18, 18, 18, 18, 18, 18, 6, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 871) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1) `ZINC000911261155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911261155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000911261155 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(N=S2(=O)CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 15, 18, 19, 19, 19, 19, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911261155 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911261155 Building ZINC000911295186 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911295186 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/872 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1) `ZINC000911295186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911295186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000911295186 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/873 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1) `ZINC000911295186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911295186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000911295186 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911295186 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 Building ZINC000911295186 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911295186 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 872) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1) `ZINC000911295186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911295186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000911295186 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 873) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1) `ZINC000911295186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911295186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000911295186 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3c(s2)CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 14, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 4, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911295186 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911295186 Building ZINC000103047491 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103047491 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/874 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1) `ZINC000103047491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103047491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000103047491 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 10, 16, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 16, 16, 50, 50, 50, 50, 5, 5, 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]) total number of confs: 101 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/875 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1) `ZINC000103047491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103047491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000103047491 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 10, 16, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 16, 16, 50, 50, 50, 50, 5, 5, 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]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103047491 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 Building ZINC000103047491 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103047491 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 874) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1) `ZINC000103047491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103047491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000103047491 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 10, 16, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 16, 16, 50, 50, 50, 50, 5, 5, 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]) total number of confs: 101 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 875) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1) `ZINC000103047491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103047491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000103047491 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 10, 16, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 16, 16, 50, 50, 50, 50, 5, 5, 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]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103047491 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103047491 Building ZINC000103050394 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103050394 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/876 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103050394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050394 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 14, 14, 42, 42, 49, 49, 42, 49, 49, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 49, 49, 42, 49, 49, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/877 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103050394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050394 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 14, 14, 38, 38, 50, 50, 38, 50, 50, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 50, 50, 38, 50, 50, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103050394 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 Building ZINC000103050394 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103050394 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 876) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103050394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050394 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 5, 14, 14, 42, 42, 49, 49, 42, 49, 49, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 49, 49, 42, 49, 49, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 877) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103050394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050394 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 14, 14, 38, 38, 50, 50, 38, 50, 50, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 50, 50, 38, 50, 50, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103050394 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050394 Building ZINC000103050395 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103050395 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/878 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103050395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050395 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 13, 13, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 50, 50, 50, 50, 50, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/879 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103050395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050395 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 14, 14, 42, 42, 49, 49, 42, 49, 49, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 49, 49, 42, 49, 49, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103050395 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 Building ZINC000103050395 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000103050395 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 878) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000103050395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050395 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 13, 13, 37, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 50, 50, 50, 50, 50, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 879) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)cc1) `ZINC000103050395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000103050395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000103050395 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2)C(F)(F)F)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 14, 14, 42, 42, 49, 49, 42, 49, 49, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 49, 49, 42, 49, 49, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000103050395 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000103050395 Building ZINC000106710764 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106710764 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/880 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106710764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710764 none Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 22, 6, 22, 22, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 22, 22, 22, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/881 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106710764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710764 none Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 23, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 23, 23, 23, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000106710764 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 Building ZINC000106710764 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106710764 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 880) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106710764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710764 none Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 22, 6, 22, 22, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 22, 22, 22, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 881) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106710764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710764 none Cc1nc(C)c([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 23, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 23, 23, 23, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000106710764 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710764 Building ZINC000106710766 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106710766 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/882 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106710766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710766 none Cc1nc(C)c([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 23, 7, 23, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/883 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C)c([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106710766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710766 none Cc1nc(C)c([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 22, 22, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 22, 22, 22, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000106710766 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 Building ZINC000106710766 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106710766 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 882) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(C)c([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106710766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710766 none Cc1nc(C)c([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 23, 7, 23, 23, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 883) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1nc(C)c([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000106710766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106710766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000106710766 none Cc1nc(C)c([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 22, 22, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 22, 22, 22, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000106710766 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000106710766 Building ZINC000108983001 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108983001 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/884 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1) `ZINC000108983001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108983001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983001 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 20, 20, 20, 30, 37, 37, 37, 37, 41, 37, 37, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 30, 30, 37, 37, 41, 41, 41, 37, 37] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/885 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1) `ZINC000108983001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108983001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983001 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 16, 27, 34, 34, 34, 34, 41, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 27, 27, 34, 34, 41, 41, 41, 34, 34] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108983001 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 Building ZINC000108983001 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108983001 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 884) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1) `ZINC000108983001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108983001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983001 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 20, 20, 20, 30, 37, 37, 37, 37, 41, 37, 37, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 30, 30, 37, 37, 41, 41, 41, 37, 37] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 885) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1) `ZINC000108983001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108983001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983001 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 16, 27, 34, 34, 34, 34, 41, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 27, 27, 34, 34, 41, 41, 41, 34, 34] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108983001 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983001 Building ZINC000108983004 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108983004 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/886 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1) `ZINC000108983004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108983004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983004 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 16, 27, 34, 34, 27, 27, 41, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 27, 27, 34, 34, 41, 41, 41, 34, 34] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/887 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1) `ZINC000108983004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108983004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983004 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 21, 21, 21, 31, 38, 38, 38, 38, 42, 38, 38, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 31, 31, 38, 38, 42, 42, 42, 38, 38] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108983004 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 Building ZINC000108983004 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108983004 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 886) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1) `ZINC000108983004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108983004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983004 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 16, 16, 16, 27, 34, 34, 27, 27, 41, 34, 34, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 27, 27, 34, 34, 41, 41, 41, 34, 34] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 887) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1) `ZINC000108983004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108983004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000108983004 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 21, 21, 21, 31, 38, 38, 38, 38, 42, 38, 38, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 31, 31, 38, 38, 42, 42, 42, 38, 38] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000108983004 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000108983004 Building ZINC000110301095 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110301095 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/888 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000110301095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110301095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000110301095 none CC(C)(C)CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 11, 16, 16, 8, 4, 8, 14, 14, 14, 14, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8] 35 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]) total number of confs: 98 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/889 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000110301095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110301095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000110301095 none CC(C)(C)CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 13, 5, 3, 5, 10, 10, 10, 10, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8] 32 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110301095 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 Building ZINC000110301095 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110301095 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 888) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000110301095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110301095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000110301095 none CC(C)(C)CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 11, 16, 16, 8, 4, 8, 14, 14, 14, 14, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8] 35 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]) total number of confs: 98 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 889) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000110301095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110301095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000110301095 none CC(C)(C)CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 13, 5, 3, 5, 10, 10, 10, 10, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8] 32 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]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110301095 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110301095 Building ZINC000110483191 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110483191 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/890 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110483191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483191 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 9, 30, 30, 30, 30, 30, 48, 48, 48, 48, 48, 48, 30, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 48, 48, 48, 48, 30, 30, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/891 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110483191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483191 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 1, 1, 1, 1, 6, 10, 29, 29, 29, 29, 29, 49, 49, 29, 29, 49, 49, 29, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 49, 49, 49, 49, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110483191 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 Building ZINC000110483191 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110483191 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 890) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110483191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483191 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 9, 30, 30, 30, 30, 30, 48, 48, 48, 48, 48, 48, 30, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 48, 48, 48, 48, 30, 30, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 891) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110483191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483191 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 5, 1, 1, 1, 1, 6, 10, 29, 29, 29, 29, 29, 49, 49, 29, 29, 49, 49, 29, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 49, 49, 49, 49, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110483191 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483191 Building ZINC000110483194 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110483194 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/892 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110483194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483194 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 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]) total number of confs: 151 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/893 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110483194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483194 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 4, 8, 29, 29, 29, 29, 29, 48, 48, 29, 29, 48, 48, 29, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 48, 48, 48, 48, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110483194 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 Building ZINC000110483194 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110483194 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 892) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110483194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483194 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 9, 29, 29, 29, 29, 29, 50, 50, 29, 29, 50, 50, 29, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 50, 50, 50, 50, 29, 29, 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]) total number of confs: 151 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 893) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1) `ZINC000110483194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110483194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000110483194 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3ccc(Cl)cc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 4, 8, 29, 29, 29, 29, 29, 48, 48, 29, 29, 48, 48, 29, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 48, 48, 48, 48, 29, 29, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000110483194 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000110483194 Building ZINC000115111861 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115111861 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/894 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C) `ZINC000115111861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115111861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000115111861 none Cc1cccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7] dock color type numbers: [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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/895 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C) `ZINC000115111861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115111861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000115111861 none Cc1cccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7] dock color type numbers: [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] 0 hydrogens 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, 19, 9, 5, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 18, 18, 19, 19, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000115111861 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 Building ZINC000115111861 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115111861 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 894) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C) `ZINC000115111861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115111861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000115111861 none Cc1cccnc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7] dock color type numbers: [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] 0 hydrogens 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, 11, 6, 11, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 895) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C) `ZINC000115111861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115111861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000115111861 none Cc1cccnc1[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7] dock color type numbers: [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] 0 hydrogens 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, 19, 9, 5, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 18, 18, 19, 19, 19, 19, 19, 19, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000115111861 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000115111861 Building ZINC000117655802 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117655802 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/896 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000117655802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117655802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000117655802 none O=C(N(CC(F)(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 23, 23, 23, 23, 11, 21, 21, 15, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5] 47 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/897 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000117655802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117655802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000117655802 none O=C(N(CC(F)(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 11, 23, 23, 23, 23, 11, 20, 20, 11, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 20, 20, 14, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5] 46 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000117655802 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 Building ZINC000117655802 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117655802 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 896) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(CC(F)(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000117655802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117655802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000117655802 none O=C(N(CC(F)(F)F)c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 23, 23, 23, 23, 11, 21, 21, 15, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5] 47 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 897) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(N(CC(F)(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000117655802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117655802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000117655802 none O=C(N(CC(F)(F)F)c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 11, 23, 23, 23, 23, 11, 20, 20, 11, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 20, 20, 14, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5] 46 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000117655802 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000117655802 Building ZINC000123028928 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123028928 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/898 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000123028928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123028928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000123028928 none CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 15, 15, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/899 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000123028928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123028928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000123028928 none CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 25, 25, 25, 25, 25, 25, 25, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 14, 14, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000123028928 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 Building ZINC000123028928 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123028928 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 898) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000123028928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123028928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000123028928 none CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 15, 15, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 899) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000123028928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123028928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000123028928 none CN(Cc1ccc(Cl)c(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 25, 25, 25, 25, 25, 25, 25, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 14, 14, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000123028928 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000123028928 Building ZINC000128725355 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128725355 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/900 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21) `ZINC000128725355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128725355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000128725355 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/901 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21) `ZINC000128725355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128725355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000128725355 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000128725355 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 Building ZINC000128725355 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128725355 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 900) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21) `ZINC000128725355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128725355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000128725355 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 901) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21) `ZINC000128725355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128725355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000128725355 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc2ncccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000128725355 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128725355 Building ZINC000128749606 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128749606 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/902 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1) `ZINC000128749606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128749606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000128749606 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 28, 28, 28, 28, 12, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/903 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1) `ZINC000128749606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128749606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000128749606 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000128749606 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 Building ZINC000128749606 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128749606 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 902) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1) `ZINC000128749606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128749606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000128749606 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 28, 28, 28, 28, 12, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 903) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1) `ZINC000128749606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128749606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000128749606 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1c1ncco1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000128749606 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000128749606 Building ZINC000129308769 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129308769 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/904 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000129308769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129308769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000129308769 none O=C(Nc1ccc(SC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 29, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/905 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(SC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000129308769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129308769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000129308769 none O=C(Nc1ccc(SC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 27, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000129308769 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 Building ZINC000129308769 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000129308769 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 904) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(Nc1ccc(SC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000129308769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000129308769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000129308769 none O=C(Nc1ccc(SC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 29, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 905) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(Nc1ccc(SC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000129308769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000129308769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000129308769 none O=C(Nc1ccc(SC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 27, 31, 31, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000129308769 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000129308769 Building ZINC000131580766 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000131580766 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/906 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1c1nsc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n1) `ZINC000131580766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000131580766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000131580766 none Cc1ccsc1c1nsc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 50, 50, 50, 50, 50, 6, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/907 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1c1nsc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n1) `ZINC000131580766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000131580766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000131580766 none Cc1ccsc1c1nsc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 50, 50, 50, 50, 50, 6, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000131580766 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 Building ZINC000131580766 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000131580766 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 906) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccsc1c1nsc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n1) `ZINC000131580766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000131580766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000131580766 none Cc1ccsc1c1nsc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 50, 50, 50, 50, 50, 6, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 907) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccsc1c1nsc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n1) `ZINC000131580766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000131580766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000131580766 none Cc1ccsc1c1nsc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 50, 50, 50, 50, 50, 6, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000131580766 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000131580766 Building ZINC000134711147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000134711147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/908 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000134711147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711147 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 4, 4, 11, 11, 11, 11, 11, 4, 6, 6, 6, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/909 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000134711147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711147 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 86 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000134711147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 Building ZINC000134711147 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000134711147 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 908) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000134711147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711147 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 4, 4, 11, 11, 11, 11, 11, 4, 6, 6, 6, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 909) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000134711147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711147 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 86 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000134711147 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711147 Building ZINC000134711167 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000134711167 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/910 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000134711167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711167 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 86 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/911 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000134711167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711167 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 95 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000134711167 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 Building ZINC000134711167 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000134711167 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 910) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000134711167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711167 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 86 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 911) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1) `ZINC000134711167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000134711167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000134711167 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2ccccc2Cl)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 95 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000134711167 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000134711167 Building ZINC000911597859 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911597859 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/912 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1) `ZINC000911597859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911597859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911597859 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 22, 22, 14, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 22, 14, 22] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/913 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1) `ZINC000911597859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911597859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911597859 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 20, 20, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 14, 20] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911597859 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 Building ZINC000911597859 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911597859 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 912) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1) `ZINC000911597859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911597859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911597859 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 22, 22, 14, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 22, 14, 22] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 913) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1) `ZINC000911597859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911597859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000911597859 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1Sc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 20, 20, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 20, 14, 20] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911597859 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911597859 Building ZINC000911922021 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911922021 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/914 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21) `ZINC000911922021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911922021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000911922021 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 2, 11, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 16, 18, 18, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 15, 15] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/915 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21) `ZINC000911922021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911922021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000911922021 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 13, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 16, 17, 17, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 16, 16] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911922021 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 Building ZINC000911922021 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000911922021 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 914) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21) `ZINC000911922021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000911922021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000911922021 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 2, 11, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 16, 18, 18, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 15, 15] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 915) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21) `ZINC000911922021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000911922021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000911922021 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2O[C@H](c3ccccc3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 2, 13, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 16, 17, 17, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 16, 16] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000911922021 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000911922021 Building ZINC000912173641 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912173641 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/916 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1) `ZINC000912173641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912173641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912173641 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 14, 18, 19, 19, 18, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/917 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1) `ZINC000912173641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912173641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912173641 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 13, 18, 19, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912173641 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 Building ZINC000912173641 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912173641 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 916) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1) `ZINC000912173641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912173641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912173641 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 14, 18, 19, 19, 18, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 917) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1) `ZINC000912173641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912173641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912173641 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccnc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 13, 18, 19, 19, 19, 19, 19, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 18, 18, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912173641 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912173641 Building ZINC000912513651 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912513651 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/918 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12) `ZINC000912513651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912513651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000912513651 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/919 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12) `ZINC000912513651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912513651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000912513651 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912513651 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 Building ZINC000912513651 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912513651 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 918) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12) `ZINC000912513651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912513651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000912513651 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 919) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12) `ZINC000912513651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912513651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000912513651 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c2ncccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20, 20] 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]) total number of confs: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912513651 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912513651 Building ZINC000912523522 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912523522 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/920 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1) `ZINC000912523522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912523522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000912523522 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/921 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1) `ZINC000912523522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912523522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000912523522 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912523522 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 Building ZINC000912523522 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912523522 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 920) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1) `ZINC000912523522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912523522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000912523522 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 921) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1) `ZINC000912523522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912523522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000912523522 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2cccc(OC)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 2, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 2] 50 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10] set([0, 1, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912523522 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912523522 Building ZINC000912708548 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912708548 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/922 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1) `ZINC000912708548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912708548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708548 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 14, 14, 14, 14, 14, 20, 20, 16, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 20, 20, 20, 20] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/923 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1) `ZINC000912708548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912708548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708548 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 18, 18, 11, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18] 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]) total number of confs: 60 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912708548 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 Building ZINC000912708548 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912708548 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 922) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1) `ZINC000912708548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912708548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708548 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 14, 14, 14, 14, 14, 20, 20, 16, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 20, 20, 20, 20] 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]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 923) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1) `ZINC000912708548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912708548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708548 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 18, 18, 11, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18] 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]) total number of confs: 60 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912708548 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708548 Building ZINC000912708549 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912708549 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/924 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1) `ZINC000912708549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912708549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708549 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18] 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]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/925 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1) `ZINC000912708549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912708549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708549 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 15, 15, 15, 15, 15, 21, 21, 20, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 21, 21] 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]) total number of confs: 52 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912708549 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 Building ZINC000912708549 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912708549 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 924) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1) `ZINC000912708549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912708549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708549 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 18, 18, 18, 18] 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]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 925) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1) `ZINC000912708549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912708549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000912708549 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 15, 15, 15, 15, 15, 21, 21, 20, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 21, 21, 21, 21] 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]) total number of confs: 52 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912708549 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912708549 Building ZINC000912999199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912999199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/926 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2) `ZINC000912999199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912999199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000912999199 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/927 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2) `ZINC000912999199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912999199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000912999199 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912999199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 Building ZINC000912999199 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000912999199 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 926) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2) `ZINC000912999199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912999199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000912999199 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 927) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2) `ZINC000912999199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912999199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000912999199 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2n1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000912999199 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000912999199 Building ZINC000913150173 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913150173 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/928 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000913150173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913150173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913150173 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14] 40 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]) total number of confs: 59 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/929 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000913150173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913150173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913150173 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 39 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]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913150173 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 Building ZINC000913150173 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913150173 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 928) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000913150173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913150173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913150173 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14] 40 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]) total number of confs: 59 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 929) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1) `ZINC000913150173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913150173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913150173 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 1, 10, 10, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 39 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]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913150173 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913150173 Building ZINC000913163740 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913163740 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/930 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1) `ZINC000913163740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913163740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913163740 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/931 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1) `ZINC000913163740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913163740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913163740 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913163740 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 Building ZINC000913163740 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913163740 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 930) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1) `ZINC000913163740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913163740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913163740 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 931) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1) `ZINC000913163740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913163740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913163740 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2cc(C(F)(F)F)ccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913163740 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913163740 Building ZINC000913345105 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345105 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/932 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345105 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 7, 7, 7, 15, 15, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 78 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/933 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345105 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 6, 15, 18, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345105 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 Building ZINC000913345105 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345105 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 932) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345105 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 7, 7, 7, 15, 15, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 78 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 933) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345105 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 6, 15, 18, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345105 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345105 Building ZINC000913345106 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345106 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/934 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345106 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 15, 20, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/935 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345106 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 8, 8, 8, 13, 13, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345106 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 Building ZINC000913345106 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345106 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 934) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345106 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 15, 20, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 15, 15, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 935) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345106 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 8, 8, 8, 13, 13, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345106 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345106 Building ZINC000913345107 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345107 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/936 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345107 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 7, 7, 16, 18, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 16, 16, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/937 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345107 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 7, 7, 7, 14, 16, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 14, 14, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 79 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345107 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 Building ZINC000913345107 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345107 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 936) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345107 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 7, 7, 16, 18, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 16, 16, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 937) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21) `ZINC000913345107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345107 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 7, 7, 7, 14, 16, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 14, 14, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 79 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345107 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345107 Building ZINC000913345108 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345108 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/938 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345108 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 7, 7, 7, 12, 12, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/939 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345108 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 7, 7, 7, 15, 18, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345108 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 Building ZINC000913345108 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913345108 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 938) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913345108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345108 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 6, 7, 7, 7, 12, 12, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 939) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21) `ZINC000913345108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913345108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000913345108 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N([C@@H](C)COC)[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 7, 7, 7, 15, 18, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913345108 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913345108 Building ZINC000913423934 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913423934 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/940 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1) `ZINC000913423934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913423934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913423934 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 2, 7, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/941 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1) `ZINC000913423934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913423934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913423934 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913423934 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 Building ZINC000913423934 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913423934 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 940) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1) `ZINC000913423934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913423934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913423934 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 1, 12, 12, 1, 1, 2, 7, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 941) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1) `ZINC000913423934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913423934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000913423934 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C(F)(F)F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 1, 1, 2, 8, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913423934 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913423934 Building ZINC000913722823 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913722823 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/942 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1) `ZINC000913722823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913722823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000913722823 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 27, 27, 11, 11, 18, 18, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 27, 27, 27, 27, 27, 18, 18, 11, 18, 18] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/943 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1) `ZINC000913722823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913722823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000913722823 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 28, 28, 11, 11, 23, 23, 11, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 28, 28, 28, 28, 28, 23, 23, 11, 23, 23] 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]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913722823 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 Building ZINC000913722823 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913722823 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 942) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1) `ZINC000913722823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913722823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000913722823 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 27, 27, 11, 11, 18, 18, 11, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 27, 27, 27, 27, 27, 18, 18, 11, 18, 18] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 943) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1) `ZINC000913722823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913722823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000913722823 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C2CC2)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 28, 28, 11, 11, 23, 23, 11, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 28, 28, 28, 28, 28, 23, 23, 11, 23, 23] 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]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913722823 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913722823 Building ZINC000913818795 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913818795 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/944 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC) `ZINC000913818795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913818795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818795 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 15, 18, 18, 18, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 19, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/945 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC) `ZINC000913818795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913818795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818795 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 16, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913818795 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 Building ZINC000913818795 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913818795 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 944) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC) `ZINC000913818795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913818795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818795 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 15, 18, 18, 18, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 19, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 945) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC) `ZINC000913818795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913818795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818795 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 16, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913818795 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818795 Building ZINC000913818796 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913818796 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/946 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC) `ZINC000913818796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913818796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818796 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/947 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC) `ZINC000913818796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913818796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818796 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 16, 17, 17, 17, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 18, 18, 18] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913818796 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 Building ZINC000913818796 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000913818796 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 946) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC) `ZINC000913818796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000913818796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818796 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 15, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 947) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC) `ZINC000913818796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000913818796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000913818796 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCSC[C@@H]1c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 16, 17, 17, 17, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 18, 18, 18] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000913818796 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000913818796 Building ZINC000916082736 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916082736 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/948 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000916082736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000916082736 none COC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 19, 48, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/949 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000916082736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000916082736 none COC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 21, 48, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 48, 48, 48, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000916082736 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 Building ZINC000916082736 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916082736 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 948) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000916082736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000916082736 none COC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 19, 48, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 949) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: COC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000916082736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916082736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000916082736 none COC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 21, 48, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 48, 48, 48, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000916082736 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000916082736 Building ZINC000773324568 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000773324568 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/950 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)CC2)cc1) `ZINC000773324568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000773324568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000773324568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 3, 3, 1, 1, 1, 2, 9, 14, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 50, 50, 50, 19, 19, 19, 19, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/951 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)CC2)cc1) `ZINC000773324568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000773324568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000773324568 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 3, 3, 1, 1, 1, 2, 9, 15, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 50, 50, 50, 21, 21, 21, 21, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000773324568 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 Building ZINC000773324568 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000773324568 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 950) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)CC2)cc1) `ZINC000773324568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000773324568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000773324568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 3, 3, 1, 1, 1, 2, 9, 14, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 50, 50, 50, 19, 19, 19, 19, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 951) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)CC2)cc1) `ZINC000773324568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000773324568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000773324568 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC=C(c3ccc(Cl)nc3)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 3, 3, 1, 1, 1, 2, 9, 15, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 50, 50, 50, 21, 21, 21, 21, 3, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000773324568 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773324568 Building ZINC000773749217 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000773749217 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/952 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000773749217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000773749217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000773749217 none Cc1ccc2c(c1)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 12 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/953 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000773749217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000773749217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000773749217 none Cc1ccc2c(c1)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 5, 5, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 14 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000773749217 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 Building ZINC000773749217 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000773749217 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 952) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc2c(c1)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000773749217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000773749217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000773749217 none Cc1ccc2c(c1)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4] 12 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 953) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc2c(c1)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000773749217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000773749217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000773749217 none Cc1ccc2c(c1)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 2, 7, 1, 1, 1, 5, 5, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 14 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000773749217 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000773749217 Building ZINC000920340156 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920340156 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/954 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000920340156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920340156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000920340156 none O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 13, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/955 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000920340156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920340156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000920340156 none O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 14, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000920340156 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 Building ZINC000920340156 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920340156 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 954) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000920340156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920340156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000920340156 none O=C(Nc1ccnn1C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 13, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 955) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000920340156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920340156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000920340156 none O=C(Nc1ccnn1C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 11, 11, 11, 11, 14, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000920340156 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000920340156 Building ZINC000855846783 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855846783 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/956 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855846783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846783 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/957 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855846783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846783 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 3, 11, 11, 12, 12, 12, 12, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 48, 48, 48, 48, 12, 12, 12, 12, 12, 12, 12, 12] 48 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000855846783 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 Building ZINC000855846783 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855846783 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 956) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855846783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846783 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 957) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855846783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846783 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 3, 11, 11, 12, 12, 12, 12, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 48, 48, 48, 48, 12, 12, 12, 12, 12, 12, 12, 12] 48 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000855846783 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846783 Building ZINC000855846784 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855846784 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/958 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855846784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846784 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/959 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855846784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846784 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 13, 13, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000855846784 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 Building ZINC000855846784 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000855846784 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 958) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000855846784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846784 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 959) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C) `ZINC000855846784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000855846784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000855846784 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H](c2cccc(Cl)c2)OCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 2, 13, 13, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 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]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000855846784 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000855846784 Building ZINC000777852760 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777852760 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/960 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F) `ZINC000777852760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777852760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852760 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 13, 13, 10, 13, 13, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13] 13 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/961 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F) `ZINC000777852760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777852760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852760 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 10, 10, 9, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 21 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000777852760 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 Building ZINC000777852760 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777852760 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 960) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F) `ZINC000777852760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777852760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852760 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 13, 13, 10, 13, 13, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13] 13 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 961) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F) `ZINC000777852760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777852760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852760 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 7, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 10, 10, 9, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 21 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000777852760 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852760 Building ZINC000777852764 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777852764 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/962 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F) `ZINC000777852764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777852764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 18 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/963 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F) `ZINC000777852764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777852764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 14, 14, 11, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14] 14 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000777852764 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 Building ZINC000777852764 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777852764 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 962) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F) `ZINC000777852764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777852764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852764 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([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]) total number of confs: 18 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 963) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F) `ZINC000777852764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777852764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000777852764 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(c1ccccc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 14, 14, 11, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14] 14 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000777852764 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000777852764 Building ZINC000923163216 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000923163216 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/964 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12) `ZINC000923163216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000923163216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000923163216 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21] 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]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/965 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12) `ZINC000923163216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000923163216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000923163216 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20] 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]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000923163216 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 Building ZINC000923163216 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000923163216 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 964) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12) `ZINC000923163216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000923163216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000923163216 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 21] 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]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 965) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12) `ZINC000923163216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000923163216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000923163216 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1c[nH]c2ccc(Br)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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] 0 hydrogens 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, 9, 1, 9, 9, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20] 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]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000923163216 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000923163216 Building ZINC000857633438 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000857633438 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/966 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000857633438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000857633438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000857633438 none CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 8, 32, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 7, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/967 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000857633438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000857633438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000857633438 none CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 7, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000857633438 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 Building ZINC000857633438 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000857633438 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 966) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000857633438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000857633438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000857633438 none CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 8, 32, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 7, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 967) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000857633438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000857633438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000857633438 none CC(C)(C)OC(=O)c1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 7, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000857633438 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000857633438 Building ZINC000647667452 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647667452 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/968 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cn1) `ZINC000647667452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647667452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647667452 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 17, 10, 4, 10, 13, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 38, 38, 38, 38, 38, 38, 38, 17, 17, 13, 13, 22, 22, 22, 22, 22, 2, 2, 2, 2, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/969 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cn1) `ZINC000647667452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647667452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647667452 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 18, 11, 5, 11, 17, 23, 23, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 18, 18, 17, 17, 23, 23, 23, 23, 23, 2, 2, 2, 2, 37] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000647667452 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 Building ZINC000647667452 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647667452 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 968) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cn1) `ZINC000647667452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647667452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647667452 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 17, 10, 4, 10, 13, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 38, 38, 38, 38, 38, 38, 38, 17, 17, 13, 13, 22, 22, 22, 22, 22, 2, 2, 2, 2, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 969) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cn1) `ZINC000647667452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647667452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000647667452 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 18, 11, 5, 11, 17, 23, 23, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 18, 18, 17, 17, 23, 23, 23, 23, 23, 2, 2, 2, 2, 37] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000647667452 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000647667452 Building ZINC000781560965 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000781560965 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/970 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000781560965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781560965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000781560965 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 9, 18, 18, 18, 18, 26, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 9, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/971 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000781560965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781560965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000781560965 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 20, 20, 20, 20, 29, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 8, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000781560965 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 Building ZINC000781560965 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000781560965 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 970) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000781560965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781560965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000781560965 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 9, 18, 18, 18, 18, 26, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 9, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 971) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1) `ZINC000781560965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781560965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000781560965 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 8, 20, 20, 20, 20, 29, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 8, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000781560965 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000781560965 Building ZINC000924884228 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000924884228 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/972 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1) `ZINC000924884228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000924884228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000924884228 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 7, 8, 18, 18, 18, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/973 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1) `ZINC000924884228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000924884228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000924884228 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 6, 7, 17, 17, 17, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000924884228 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 Building ZINC000924884228 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000924884228 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 972) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1) `ZINC000924884228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000924884228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000924884228 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 8, 8, 7, 8, 18, 18, 18, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 973) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1) `ZINC000924884228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000924884228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000924884228 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C)C)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 6, 7, 17, 17, 17, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000924884228 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000924884228 Building ZINC000648528410 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648528410 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/974 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1) `ZINC000648528410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648528410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000648528410 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 2, 4, 7, 11, 11, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 9, 9, 7, 7, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/975 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1) `ZINC000648528410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648528410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000648528410 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 2, 3, 6, 10, 10, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648528410 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 Building ZINC000648528410 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648528410 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 974) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1) `ZINC000648528410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648528410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000648528410 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 2, 4, 7, 11, 11, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 9, 9, 7, 7, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 975) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1) `ZINC000648528410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648528410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000648528410 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 2, 3, 6, 10, 10, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648528410 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648528410 Building ZINC000648530084 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648530084 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/976 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cn1) `ZINC000648530084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648530084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000648530084 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 10, 6, 4, 6, 8, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 10, 10, 8, 8, 12, 12, 12, 12, 12, 5, 5, 21] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/977 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cn1) `ZINC000648530084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648530084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000648530084 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 12, 7, 4, 7, 10, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 12, 12, 10, 10, 13, 13, 13, 13, 13, 5, 5, 23] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648530084 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 Building ZINC000648530084 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648530084 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 976) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cn1) `ZINC000648530084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648530084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000648530084 none Cc1ccc(CN(CC2CC2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 10, 6, 4, 6, 8, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 10, 10, 8, 8, 12, 12, 12, 12, 12, 5, 5, 21] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 977) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cn1) `ZINC000648530084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648530084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000648530084 none Cc1ccc(CN(CC2CC2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.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, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 12, 7, 4, 7, 10, 13, 13, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 12, 12, 10, 10, 13, 13, 13, 13, 13, 5, 5, 23] 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648530084 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648530084 Building ZINC000648544472 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648544472 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/978 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000648544472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648544472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000648544472 none CN(CCC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 31, 31, 37, 37, 37, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 12, 12, 12, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4] 41 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/979 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000648544472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648544472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000648544472 none CN(CCC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 31, 31, 40, 41, 41, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 12, 12, 12, 31, 31, 31, 31, 40, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4] 46 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648544472 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 Building ZINC000648544472 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648544472 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 978) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(CCC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000648544472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648544472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000648544472 none CN(CCC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 31, 31, 37, 37, 37, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 12, 12, 12, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4] 41 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 979) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CN(CCC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000648544472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648544472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000648544472 none CN(CCC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 31, 31, 40, 41, 41, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 12, 12, 12, 31, 31, 31, 31, 40, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4] 46 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000648544472 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000648544472 Building ZINC000161865697 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161865697 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/980 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1) `ZINC000161865697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161865697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000161865697 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/981 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1) `ZINC000161865697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161865697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000161865697 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000161865697 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 Building ZINC000161865697 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000161865697 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 980) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1) `ZINC000161865697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000161865697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000161865697 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 981) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1) `ZINC000161865697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000161865697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000161865697 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)nc3ccc([N+](=O)[O-])cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000161865697 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000161865697 Building ZINC000727711613 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727711613 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/982 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000727711613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727711613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000727711613 none O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/983 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000727711613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727711613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000727711613 none O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 17, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000727711613 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 Building ZINC000727711613 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727711613 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 982) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000727711613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727711613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000727711613 none O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 983) grep: /scratch/xiaobo/132203/xbs-8058115.45/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(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000727711613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727711613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000727711613 none O=C(Nc1ccc([N+](=O)[O-])c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 17, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000727711613 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000727711613 Building ZINC000556483803 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000556483803 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/984 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-]) `ZINC000556483803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000556483803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000556483803 none CC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 6, 6, 6, 6, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/985 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-]) `ZINC000556483803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000556483803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000556483803 none CC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 27, 45, 45, 26, 45, 45, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 4, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 6, 6, 6, 6, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000556483803 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 Building ZINC000556483803 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000556483803 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 984) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-]) `ZINC000556483803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000556483803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000556483803 none CC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 6, 6, 6, 6, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 985) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-]) `ZINC000556483803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000556483803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000556483803 none CC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 27, 45, 45, 26, 45, 45, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 4, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 10, 6, 6, 6, 6, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000556483803 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000556483803 Building ZINC000487694770 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487694770 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/986 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487694770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694770 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 16, 34, 34, 34, 34, 34, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 34, 34, 17, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/987 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487694770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694770 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 34, 34, 12, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 4, 3, 3, 3, 3, 34, 34, 15, 34] 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]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000487694770 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 Building ZINC000487694770 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487694770 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 986) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487694770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694770 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 16, 34, 34, 34, 34, 34, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 34, 34, 17, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 987) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487694770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694770 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 34, 34, 12, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 4, 3, 3, 3, 3, 34, 34, 15, 34] 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]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000487694770 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694770 Building ZINC000487694773 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487694773 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/988 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487694773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694773 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 15, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 4, 3, 3, 3, 3, 34, 34, 16, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/989 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487694773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694773 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 34, 34, 34, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000487694773 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 Building ZINC000487694773 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487694773 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 988) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487694773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694773 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 15, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 4, 3, 3, 3, 3, 34, 34, 16, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 989) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1) `ZINC000487694773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487694773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000487694773 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 34, 34, 34, 34] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000487694773 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000487694773 Building ZINC000754286635 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754286635 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/990 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754286635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754286635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000754286635 none Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 26, 43, 43, 43, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 2, 6, 6, 43, 43, 43, 43, 43, 11, 6, 6, 6, 6] 47 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/991 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754286635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754286635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000754286635 none Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 21, 26, 43, 43, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 43, 11, 6, 6, 6, 6] 47 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754286635 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 Building ZINC000754286635 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754286635 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 990) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754286635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754286635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000754286635 none Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 26, 43, 43, 43, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 2, 6, 6, 43, 43, 43, 43, 43, 11, 6, 6, 6, 6] 47 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 991) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000754286635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754286635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000754286635 none Cc1cc(Cl)c([N+](=O)[O-])cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 21, 26, 43, 43, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 43, 43, 43, 43, 43, 11, 6, 6, 6, 6] 47 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000754286635 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000754286635 Building ZINC000170732408 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170732408 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/992 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000170732408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170732408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000170732408 none CCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 4, 2, 4, 10, 18, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 10, 10, 10, 10, 18, 18, 18, 18, 36, 5, 5, 5, 5, 5, 5, 5, 5, 5] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/993 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000170732408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170732408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000170732408 none CCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 4, 2, 4, 11, 19, 19, 19, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 10, 10, 11, 11, 19, 19, 19, 19, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000170732408 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 Building ZINC000170732408 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170732408 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 992) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000170732408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170732408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000170732408 none CCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 4, 2, 4, 10, 18, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 10, 10, 10, 10, 18, 18, 18, 18, 36, 5, 5, 5, 5, 5, 5, 5, 5, 5] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 993) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000170732408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170732408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000170732408 none CCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 10, 4, 2, 4, 11, 19, 19, 19, 19, 19, 19, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 10, 10, 11, 11, 19, 19, 19, 19, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000170732408 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000170732408 Building ZINC000800914549 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000800914549 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/994 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000800914549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000800914549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000800914549 none CCCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 16, 13, 5, 2, 5, 16, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 21, 22, 17, 17, 13, 13, 16, 16, 26, 26, 26, 26, 52, 3, 3, 3, 3] 100 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]) total number of confs: 223 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/995 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000800914549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000800914549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000800914549 none CCCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 14, 6, 3, 6, 17, 27, 27, 27, 27, 27, 27, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 22, 18, 18, 14, 14, 17, 17, 27, 27, 27, 27, 54, 3, 3, 3, 3] 100 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]) total number of confs: 227 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000800914549 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 Building ZINC000800914549 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000800914549 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 994) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000800914549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000800914549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000800914549 none CCCCN(Cc1ccccc1O)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 16, 13, 5, 2, 5, 16, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 21, 22, 17, 17, 13, 13, 16, 16, 26, 26, 26, 26, 52, 3, 3, 3, 3] 100 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]) total number of confs: 223 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 995) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000800914549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000800914549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000800914549 none CCCCN(Cc1ccccc1O)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 14, 6, 3, 6, 17, 27, 27, 27, 27, 27, 27, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 22, 18, 18, 14, 14, 17, 17, 27, 27, 27, 27, 54, 3, 3, 3, 3] 100 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]) total number of confs: 227 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000800914549 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000800914549 Building ZINC000730109958 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730109958 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/996 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000730109958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730109958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730109958 none CCN(CC)c1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 9, 20, 39, 9, 12, 12, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 12, 12, 9, 9, 4, 4, 4, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/997 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000730109958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730109958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730109958 none CCN(CC)c1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 20, 40, 9, 12, 12, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 12, 12, 9, 9, 4, 4, 4, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000730109958 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 Building ZINC000730109958 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730109958 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 996) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(CC)c1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000730109958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730109958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730109958 none CCN(CC)c1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 9, 20, 39, 9, 12, 12, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 12, 12, 9, 9, 4, 4, 4, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 997) grep: /scratch/xiaobo/132203/xbs-8058115.45/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: CCN(CC)c1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000730109958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730109958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730109958 none CCN(CC)c1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 20, 40, 9, 12, 12, 9, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 12, 12, 9, 9, 4, 4, 4, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000730109958 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730109958 Building ZINC000730110722 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730110722 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/998 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000730110722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730110722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730110722 none CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 22, 6, 15, 32, 42, 42, 32, 33, 49, 49, 42, 42, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 22, 22, 32, 32, 42, 42, 49, 49, 49, 49, 49, 49, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/999 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000730110722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730110722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730110722 none CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 15, 23, 6, 15, 32, 42, 42, 32, 32, 50, 50, 42, 42, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 23, 23, 23, 23, 32, 32, 42, 42, 50, 50, 50, 50, 50, 50, 42, 42, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000730110722 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 Building ZINC000730110722 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730110722 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 998) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000730110722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730110722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730110722 none CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 22, 6, 15, 32, 42, 42, 32, 33, 49, 49, 42, 42, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 22, 22, 32, 32, 42, 42, 49, 49, 49, 49, 49, 49, 42, 42, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 278 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 mkdir: created directory `1' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 1 (index: 999) grep: /scratch/xiaobo/132203/xbs-8058115.45/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000730110722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730110722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000730110722 none CC(C)N(Cc1ccc(N(C)C)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 15, 23, 6, 15, 32, 42, 42, 32, 32, 50, 50, 42, 42, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 23, 23, 23, 23, 23, 32, 32, 42, 42, 50, 50, 50, 50, 50, 50, 42, 42, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000730110722 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 1: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/1.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000730110722 Building ZINC000901054587 mkdir: created directory `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000901054587 mkdir: created directory `0' /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587/0 /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/132203/xbs-8058115.45/working/3D/1000 `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccccc1O) `ZINC000901054587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000901054587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000901054587 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)Cc1ccccc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 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, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 6, 9, 9, 9, 9, 4, 7, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 7, 7, 10, 10, 10, 10, 20] 100 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]) total number of confs: 78 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587 /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Finished preparing ZINC000901054587 Recording results /scratch/xiaobo/132203/xbs-8058115.45/working /scratch/xiaobo/132203/xbs-8058115.45 Appending to /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.* 0: /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587/0.* Removing working files in /scratch/xiaobo/132203/xbs-8058115.45/working/building/ZINC000901054587 /scratch/xiaobo/132203/xbs-8058115.45 Compressing combined databse files /scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/132203/xbs-8058115.45/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/132203/xbs-8058115.45/working/3D/1001' removed directory: `/scratch/xiaobo/132203/xbs-8058115.45/working/3D' rmdir: removing directory, `/scratch/xiaobo/132203/xbs-8058115.45/working/building' rmdir: removing directory, `/scratch/xiaobo/132203/xbs-8058115.45/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/132203/xbs-8058115.45' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbs' `/scratch/xiaobo/132203/xbs-8058115.45/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbs/finished' `/scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbs/finished/xbs.db2.gz' removed `/scratch/xiaobo/132203/xbs-8058115.45/finished/xbs.db2.gz' removed directory: `/scratch/xiaobo/132203/xbs-8058115.45/finished' removed directory: `/scratch/xiaobo/132203/xbs-8058115.45'